HEADER HYDROLASE 21-SEP-18 6HPU
TITLE CRYSTAL STRUCTURE OF HUMAN PIF1 HELICASE IN COMPLEX WITH ADP-ALF4
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ATP-DEPENDENT DNA HELICASE PIF1;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: DNA REPAIR AND RECOMBINATION HELICASE PIF1,PIF1/RRM3 DNA
COMPND 5 HELICASE-LIKE PROTEIN;
COMPND 6 EC: 3.6.4.12;
COMPND 7 ENGINEERED: YES;
COMPND 8 OTHER_DETAILS: SRM - CLONING ARTEFACT
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PIF1, C15ORF20;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET
KEYWDS PIF1, 5'-3' DNA HELICASE, DUPLEX UNWINDING, TELOMERE MAINTENANCE, DNA
KEYWDS 2 REPAIR, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR V.M.LEVDIKOV,S.DEHGHANI-TAFTI,B.D.BAX,C.M.SANDERS,A.A.ANTSON
REVDAT 4 24-JAN-24 6HPU 1 REMARK
REVDAT 3 17-APR-19 6HPU 1 JRNL
REVDAT 2 13-FEB-19 6HPU 1 JRNL
REVDAT 1 23-JAN-19 6HPU 0
JRNL AUTH S.DEHGHANI-TAFTI,V.LEVDIKOV,A.A.ANTSON,B.BAX,C.M.SANDERS
JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE NUCLEOTIDE AND DNA
JRNL TITL 2 BINDING ACTIVITIES OF THE HUMAN PIF1 HELICASE.
JRNL REF NUCLEIC ACIDS RES. V. 47 3208 2019
JRNL REFN ESSN 1362-4962
JRNL PMID 30698796
JRNL DOI 10.1093/NAR/GKZ028
REMARK 2
REMARK 2 RESOLUTION. 3.96 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0222
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.96
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 91.03
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 16607
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.179
REMARK 3 R VALUE (WORKING SET) : 0.175
REMARK 3 FREE R VALUE : 0.253
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600
REMARK 3 FREE R VALUE TEST SET COUNT : 794
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.96
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.06
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1134
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.06
REMARK 3 BIN R VALUE (WORKING SET) : 0.3330
REMARK 3 BIN FREE R VALUE SET COUNT : 85
REMARK 3 BIN FREE R VALUE : 0.3950
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6359
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 66
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 151.7
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 151.6
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -5.50000
REMARK 3 B22 (A**2) : -5.50000
REMARK 3 B33 (A**2) : 17.84000
REMARK 3 B12 (A**2) : -2.75000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.638
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.487
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 37.623
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6610 ; 0.010 ; 0.014
REMARK 3 BOND LENGTHS OTHERS (A): 6048 ; 0.001 ; 0.017
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8972 ; 1.558 ; 1.666
REMARK 3 BOND ANGLES OTHERS (DEGREES): 14195 ; 0.827 ; 1.630
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 854 ;10.022 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 353 ;36.469 ;20.085
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1147 ;22.319 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 72 ;18.578 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 855 ; 0.066 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7511 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1159 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3356 ;13.905 ;15.539
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3355 ;13.904 ;15.538
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4197 ;21.394 ;23.243
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4198 ;21.393 ;23.245
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3252 ;13.590 ;16.127
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3249 ;13.578 ;16.133
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4759 ;21.075 ;23.890
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 26391 ;31.397 ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 26389 ;31.394 ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 6HPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-SEP-18.
REMARK 100 THE DEPOSITION ID IS D_1200012047.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-DEC-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6-8
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2
REMARK 200 DATA SCALING SOFTWARE : XIA2
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17663
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.960
REMARK 200 RESOLUTION RANGE LOW (A) : 104.930
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 12.30
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.96
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.06
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 12.80
REMARK 200 R MERGE FOR SHELL (I) : 0.85700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 6HPH
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 77.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.51
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: MES, CA-ACETATE, PEG 20K, PEG550 MME,
REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 274K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.59000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.29500
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 26.29500
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.59000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 SER B 619
REMARK 465 LEU B 620
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 OG SER B 235 MG MG B 803 1.66
REMARK 500 OE2 GLU A 307 F3 ALF A 802 2.05
REMARK 500 OE2 GLU B 307 F3 ALF B 802 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG B 398 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 SER A 229 -179.27 -64.19
REMARK 500 SER A 255 -82.38 -46.15
REMARK 500 CYS A 261 -16.86 -49.73
REMARK 500 CYS A 300 112.60 -37.42
REMARK 500 GLU A 307 80.91 42.68
REMARK 500 ALA A 325 -76.68 -61.05
REMARK 500 ASN A 330 50.43 -95.37
REMARK 500 PHE A 333 31.18 73.30
REMARK 500 GLN A 346 -114.51 -74.21
REMARK 500 SER A 354 -52.39 -130.36
REMARK 500 PRO A 371 -53.18 -27.30
REMARK 500 THR A 377 -7.27 -140.31
REMARK 500 ALA A 383 -76.40 -72.89
REMARK 500 ARG A 417 -101.06 -100.64
REMARK 500 THR A 423 -157.35 -89.94
REMARK 500 ALA A 452 -154.69 -79.16
REMARK 500 MET A 453 73.26 -171.64
REMARK 500 ALA A 460 -37.51 -38.98
REMARK 500 CYS A 467 -176.05 -66.82
REMARK 500 LEU A 477 151.57 -49.18
REMARK 500 LEU A 487 -68.11 -129.59
REMARK 500 ASP A 527 -164.09 -114.74
REMARK 500 THR A 534 97.57 -35.99
REMARK 500 ALA A 549 40.21 -106.94
REMARK 500 CYS A 564 38.95 -152.76
REMARK 500 ARG A 571 -159.03 -178.92
REMARK 500 PRO A 598 -3.89 -56.09
REMARK 500 SER A 619 -91.19 -75.21
REMARK 500 ARG B 204 -157.38 -110.70
REMARK 500 VAL B 214 -78.16 -53.08
REMARK 500 SER B 229 -165.91 -70.65
REMARK 500 LYS B 234 -72.65 -63.95
REMARK 500 GLU B 307 78.19 45.23
REMARK 500 ALA B 325 -85.24 -60.68
REMARK 500 PHE B 333 36.02 35.56
REMARK 500 GLN B 346 -106.47 -71.59
REMARK 500 LYS B 352 -74.29 -81.48
REMARK 500 ALA B 383 -81.75 -71.65
REMARK 500 CYS B 399 73.96 -102.13
REMARK 500 THR B 410 26.23 -79.31
REMARK 500 SER B 412 31.15 -96.90
REMARK 500 ARG B 417 -119.31 -116.48
REMARK 500 THR B 423 -151.29 -70.70
REMARK 500 ARG B 424 107.31 -8.55
REMARK 500 LEU B 477 85.99 -56.74
REMARK 500 ASN B 495 102.32 -58.89
REMARK 500 PHE B 504 -162.32 -124.54
REMARK 500 GLU B 507 -163.97 -117.85
REMARK 500 LEU B 511 107.96 -57.36
REMARK 500 ASP B 527 -151.74 -124.42
REMARK 500
REMARK 500 THIS ENTRY HAS 57 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 SER A 400 ASP A 401 -147.05
REMARK 500 CYS A 467 PRO A 468 147.36
REMARK 500 ASP A 563 CYS A 564 -141.78
REMARK 500 PRO B 280 LEU B 281 -146.04
REMARK 500 GLN B 328 GLN B 329 140.06
REMARK 500 LEU B 396 GLY B 397 146.51
REMARK 500 ALA B 422 THR B 423 -125.20
REMARK 500 ARG B 616 GLY B 617 145.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG A 405 0.09 SIDE CHAIN
REMARK 500 ARG A 449 0.08 SIDE CHAIN
REMARK 500 ARG B 216 0.17 SIDE CHAIN
REMARK 500 ARG B 324 0.11 SIDE CHAIN
REMARK 500 ARG B 417 0.12 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 803 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 235 OG
REMARK 620 2 GLY A 559 O 97.7
REMARK 620 3 ADP A 801 O3B 102.7 126.3
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ALF A 802
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 803
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ADP B 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ALF B 802
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 803
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6HPH RELATED DB: PDB
REMARK 900 RELATED ID: 6HPQ RELATED DB: PDB
REMARK 900 RELATED ID: 6HPT RELATED DB: PDB
DBREF 6HPU A 206 620 UNP Q9H611 PIF1_HUMAN 206 620
DBREF 6HPU B 206 620 UNP Q9H611 PIF1_HUMAN 206 620
SEQADV 6HPU SER A 203 UNP Q9H611 EXPRESSION TAG
SEQADV 6HPU ARG A 204 UNP Q9H611 EXPRESSION TAG
SEQADV 6HPU MET A 205 UNP Q9H611 EXPRESSION TAG
SEQADV 6HPU SER B 203 UNP Q9H611 EXPRESSION TAG
SEQADV 6HPU ARG B 204 UNP Q9H611 EXPRESSION TAG
SEQADV 6HPU MET B 205 UNP Q9H611 EXPRESSION TAG
SEQRES 1 A 418 SER ARG MET GLN LEU SER GLU GLU GLN ALA ALA VAL LEU
SEQRES 2 A 418 ARG ALA VAL LEU LYS GLY GLN SER ILE PHE PHE THR GLY
SEQRES 3 A 418 SER ALA GLY THR GLY LYS SER TYR LEU LEU LYS ARG ILE
SEQRES 4 A 418 LEU GLY SER LEU PRO PRO THR GLY THR VAL ALA THR ALA
SEQRES 5 A 418 SER THR GLY VAL ALA ALA CYS HIS ILE GLY GLY THR THR
SEQRES 6 A 418 LEU HIS ALA PHE ALA GLY ILE GLY SER GLY GLN ALA PRO
SEQRES 7 A 418 LEU ALA GLN CYS VAL ALA LEU ALA GLN ARG PRO GLY VAL
SEQRES 8 A 418 ARG GLN GLY TRP LEU ASN CYS GLN ARG LEU VAL ILE ASP
SEQRES 9 A 418 GLU ILE SER MET VAL GLU ALA ASP LEU PHE ASP LYS LEU
SEQRES 10 A 418 GLU ALA VAL ALA ARG ALA VAL ARG GLN GLN ASN LYS PRO
SEQRES 11 A 418 PHE GLY GLY ILE GLN LEU ILE ILE CYS GLY ASP PHE LEU
SEQRES 12 A 418 GLN LEU PRO PRO VAL THR LYS GLY SER GLN PRO PRO ARG
SEQRES 13 A 418 PHE CYS PHE GLN SER LYS SER TRP LYS ARG CYS VAL PRO
SEQRES 14 A 418 VAL THR LEU GLU LEU THR LYS VAL TRP ARG GLN ALA ASP
SEQRES 15 A 418 GLN THR PHE ILE SER LEU LEU GLN ALA VAL ARG LEU GLY
SEQRES 16 A 418 ARG CYS SER ASP GLU VAL THR ARG GLN LEU GLN ALA THR
SEQRES 17 A 418 ALA SER HIS LYS VAL GLY ARG ASP GLY ILE VAL ALA THR
SEQRES 18 A 418 ARG LEU CYS THR HIS GLN ASP ASP VAL ALA LEU THR ASN
SEQRES 19 A 418 GLU ARG ARG LEU GLN GLU LEU PRO GLY LYS VAL HIS ARG
SEQRES 20 A 418 PHE GLU ALA MET ASP SER ASN PRO GLU LEU ALA SER THR
SEQRES 21 A 418 LEU ASP ALA GLN CYS PRO VAL SER GLN LEU LEU GLN LEU
SEQRES 22 A 418 LYS LEU GLY ALA GLN VAL MET LEU VAL LYS ASN LEU SER
SEQRES 23 A 418 VAL SER ARG GLY LEU VAL ASN GLY ALA ARG GLY VAL VAL
SEQRES 24 A 418 VAL GLY PHE GLU ALA GLU GLY ARG GLY LEU PRO GLN VAL
SEQRES 25 A 418 ARG PHE LEU CYS GLY VAL THR GLU VAL ILE HIS ALA ASP
SEQRES 26 A 418 ARG TRP THR VAL GLN ALA THR GLY GLY GLN LEU LEU SER
SEQRES 27 A 418 ARG GLN GLN LEU PRO LEU GLN LEU ALA TRP ALA MET SER
SEQRES 28 A 418 ILE HIS LYS SER GLN GLY MET THR LEU ASP CYS VAL GLU
SEQRES 29 A 418 ILE SER LEU GLY ARG VAL PHE ALA SER GLY GLN ALA TYR
SEQRES 30 A 418 VAL ALA LEU SER ARG ALA ARG SER LEU GLN GLY LEU ARG
SEQRES 31 A 418 VAL LEU ASP PHE ASP PRO MET ALA VAL ARG CYS ASP PRO
SEQRES 32 A 418 ARG VAL LEU HIS PHE TYR ALA THR LEU ARG ARG GLY ARG
SEQRES 33 A 418 SER LEU
SEQRES 1 B 418 SER ARG MET GLN LEU SER GLU GLU GLN ALA ALA VAL LEU
SEQRES 2 B 418 ARG ALA VAL LEU LYS GLY GLN SER ILE PHE PHE THR GLY
SEQRES 3 B 418 SER ALA GLY THR GLY LYS SER TYR LEU LEU LYS ARG ILE
SEQRES 4 B 418 LEU GLY SER LEU PRO PRO THR GLY THR VAL ALA THR ALA
SEQRES 5 B 418 SER THR GLY VAL ALA ALA CYS HIS ILE GLY GLY THR THR
SEQRES 6 B 418 LEU HIS ALA PHE ALA GLY ILE GLY SER GLY GLN ALA PRO
SEQRES 7 B 418 LEU ALA GLN CYS VAL ALA LEU ALA GLN ARG PRO GLY VAL
SEQRES 8 B 418 ARG GLN GLY TRP LEU ASN CYS GLN ARG LEU VAL ILE ASP
SEQRES 9 B 418 GLU ILE SER MET VAL GLU ALA ASP LEU PHE ASP LYS LEU
SEQRES 10 B 418 GLU ALA VAL ALA ARG ALA VAL ARG GLN GLN ASN LYS PRO
SEQRES 11 B 418 PHE GLY GLY ILE GLN LEU ILE ILE CYS GLY ASP PHE LEU
SEQRES 12 B 418 GLN LEU PRO PRO VAL THR LYS GLY SER GLN PRO PRO ARG
SEQRES 13 B 418 PHE CYS PHE GLN SER LYS SER TRP LYS ARG CYS VAL PRO
SEQRES 14 B 418 VAL THR LEU GLU LEU THR LYS VAL TRP ARG GLN ALA ASP
SEQRES 15 B 418 GLN THR PHE ILE SER LEU LEU GLN ALA VAL ARG LEU GLY
SEQRES 16 B 418 ARG CYS SER ASP GLU VAL THR ARG GLN LEU GLN ALA THR
SEQRES 17 B 418 ALA SER HIS LYS VAL GLY ARG ASP GLY ILE VAL ALA THR
SEQRES 18 B 418 ARG LEU CYS THR HIS GLN ASP ASP VAL ALA LEU THR ASN
SEQRES 19 B 418 GLU ARG ARG LEU GLN GLU LEU PRO GLY LYS VAL HIS ARG
SEQRES 20 B 418 PHE GLU ALA MET ASP SER ASN PRO GLU LEU ALA SER THR
SEQRES 21 B 418 LEU ASP ALA GLN CYS PRO VAL SER GLN LEU LEU GLN LEU
SEQRES 22 B 418 LYS LEU GLY ALA GLN VAL MET LEU VAL LYS ASN LEU SER
SEQRES 23 B 418 VAL SER ARG GLY LEU VAL ASN GLY ALA ARG GLY VAL VAL
SEQRES 24 B 418 VAL GLY PHE GLU ALA GLU GLY ARG GLY LEU PRO GLN VAL
SEQRES 25 B 418 ARG PHE LEU CYS GLY VAL THR GLU VAL ILE HIS ALA ASP
SEQRES 26 B 418 ARG TRP THR VAL GLN ALA THR GLY GLY GLN LEU LEU SER
SEQRES 27 B 418 ARG GLN GLN LEU PRO LEU GLN LEU ALA TRP ALA MET SER
SEQRES 28 B 418 ILE HIS LYS SER GLN GLY MET THR LEU ASP CYS VAL GLU
SEQRES 29 B 418 ILE SER LEU GLY ARG VAL PHE ALA SER GLY GLN ALA TYR
SEQRES 30 B 418 VAL ALA LEU SER ARG ALA ARG SER LEU GLN GLY LEU ARG
SEQRES 31 B 418 VAL LEU ASP PHE ASP PRO MET ALA VAL ARG CYS ASP PRO
SEQRES 32 B 418 ARG VAL LEU HIS PHE TYR ALA THR LEU ARG ARG GLY ARG
SEQRES 33 B 418 SER LEU
HET ADP A 801 27
HET ALF A 802 5
HET MG A 803 1
HET ADP B 801 27
HET ALF B 802 5
HET MG B 803 1
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
HETNAM ALF TETRAFLUOROALUMINATE ION
HETNAM MG MAGNESIUM ION
FORMUL 3 ADP 2(C10 H15 N5 O10 P2)
FORMUL 4 ALF 2(AL F4 1-)
FORMUL 5 MG 2(MG 2+)
HELIX 1 AA1 SER A 208 GLY A 221 1 14
HELIX 2 AA2 GLY A 233 LEU A 245 1 13
HELIX 3 AA3 THR A 256 HIS A 262 1 7
HELIX 4 AA4 LEU A 268 GLY A 273 1 6
HELIX 5 AA5 PRO A 280 ARG A 290 1 11
HELIX 6 AA6 GLY A 292 CYS A 300 1 9
HELIX 7 AA7 GLU A 312 GLN A 328 1 17
HELIX 8 AA8 SER A 363 VAL A 370 1 8
HELIX 9 AA9 ASP A 384 GLY A 397 1 14
HELIX 10 AB1 SER A 400 THR A 410 1 11
HELIX 11 AB2 ALA A 411 HIS A 413 5 3
HELIX 12 AB3 HIS A 428 GLU A 442 1 15
HELIX 13 AB4 LEU A 459 CYS A 467 1 9
HELIX 14 AB5 ILE A 554 GLN A 558 1 5
HELIX 15 AB6 GLY A 576 SER A 583 1 8
HELIX 16 AB7 ASP A 604 HIS A 609 1 6
HELIX 17 AB8 HIS A 609 LEU A 614 1 6
HELIX 18 AB9 ARG A 615 ARG A 618 5 4
HELIX 19 AC1 SER B 208 GLY B 221 1 14
HELIX 20 AC2 GLY B 233 LEU B 245 1 13
HELIX 21 AC3 GLY B 257 GLY B 264 1 8
HELIX 22 AC4 LEU B 268 GLY B 273 1 6
HELIX 23 AC5 PRO B 280 ARG B 290 1 11
HELIX 24 AC6 GLY B 292 CYS B 300 1 9
HELIX 25 AC7 GLU B 312 GLN B 328 1 17
HELIX 26 AC8 LYS B 331 ILE B 336 5 6
HELIX 27 AC9 PHE B 359 SER B 363 5 5
HELIX 28 AD1 SER B 365 VAL B 370 1 6
HELIX 29 AD2 ASP B 384 LEU B 396 1 13
HELIX 30 AD3 SER B 400 ALA B 409 1 10
HELIX 31 AD4 THR B 410 SER B 412 5 3
HELIX 32 AD5 HIS B 428 GLN B 441 1 14
HELIX 33 AD6 ASN B 456 GLU B 458 5 3
HELIX 34 AD7 LEU B 459 CYS B 467 1 9
HELIX 35 AD8 ILE B 554 GLN B 558 1 5
HELIX 36 AD9 GLY B 576 ALA B 585 1 10
HELIX 37 AE1 SER B 587 GLN B 589 5 3
HELIX 38 AE2 ASP B 597 VAL B 601 5 5
HELIX 39 AE3 ASP B 604 ARG B 616 1 13
SHEET 1 AA1 6 THR A 266 THR A 267 0
SHEET 2 AA1 6 THR A 250 ALA A 254 1 N ALA A 252 O THR A 266
SHEET 3 AA1 6 ARG A 302 ASP A 306 1 O ARG A 302 N VAL A 251
SHEET 4 AA1 6 GLN A 337 CYS A 341 1 O ILE A 339 N LEU A 303
SHEET 5 AA1 6 PHE A 225 THR A 227 1 N PHE A 226 O ILE A 340
SHEET 6 AA1 6 THR A 373 GLU A 375 1 O LEU A 374 N THR A 227
SHEET 1 AA2 2 LEU A 425 CYS A 426 0
SHEET 2 AA2 2 MET A 552 SER A 553 1 O MET A 552 N CYS A 426
SHEET 1 AA3 2 HIS A 448 GLU A 451 0
SHEET 2 AA3 2 LEU A 472 LEU A 475 -1 O LEU A 475 N HIS A 448
SHEET 1 AA4 5 THR A 521 VAL A 523 0
SHEET 2 AA4 5 PRO A 512 PHE A 516 -1 N VAL A 514 O GLU A 522
SHEET 3 AA4 5 ALA A 497 PHE A 504 -1 N VAL A 500 O ARG A 515
SHEET 4 AA4 5 GLN A 480 LEU A 483 -1 N VAL A 481 O GLY A 499
SHEET 5 AA4 5 LEU A 546 GLN A 547 -1 O GLN A 547 N MET A 482
SHEET 1 AA5 2 ASP A 527 ALA A 533 0
SHEET 2 AA5 2 GLN A 537 GLN A 543 -1 N LEU A 539 O VAL A 531
SHEET 1 AA6 2 VAL A 565 SER A 568 0
SHEET 2 AA6 2 LEU A 591 LEU A 594 1 O LEU A 594 N ILE A 567
SHEET 1 AA7 6 THR B 266 THR B 267 0
SHEET 2 AA7 6 VAL B 251 ALA B 254 1 N ALA B 252 O THR B 266
SHEET 3 AA7 6 ARG B 302 ASP B 306 1 O VAL B 304 N VAL B 251
SHEET 4 AA7 6 GLN B 337 CYS B 341 1 O GLN B 337 N LEU B 303
SHEET 5 AA7 6 ILE B 224 GLY B 228 1 N ILE B 224 O ILE B 340
SHEET 6 AA7 6 VAL B 372 LEU B 376 1 O LEU B 374 N THR B 227
SHEET 1 AA8 2 LEU B 425 CYS B 426 0
SHEET 2 AA8 2 MET B 552 SER B 553 1 O MET B 552 N CYS B 426
SHEET 1 AA9 2 VAL B 447 HIS B 448 0
SHEET 2 AA9 2 LEU B 475 LYS B 476 -1 O LEU B 475 N HIS B 448
SHEET 1 AB1 5 THR B 521 VAL B 523 0
SHEET 2 AB1 5 GLN B 513 PHE B 516 -1 N VAL B 514 O GLU B 522
SHEET 3 AB1 5 ALA B 497 GLY B 503 -1 N GLY B 503 O GLN B 513
SHEET 4 AB1 5 GLN B 480 LEU B 483 -1 N VAL B 481 O GLY B 499
SHEET 5 AB1 5 LEU B 546 LEU B 548 -1 O GLN B 547 N MET B 482
SHEET 1 AB2 2 TRP B 529 VAL B 531 0
SHEET 2 AB2 2 LEU B 539 ARG B 541 -1 O LEU B 539 N VAL B 531
SHEET 1 AB3 2 VAL B 565 SER B 568 0
SHEET 2 AB3 2 LEU B 591 LEU B 594 1 O ARG B 592 N VAL B 565
LINK OG SER A 235 MG MG A 803 1555 1555 2.10
LINK O GLY A 559 MG MG A 803 1555 1555 2.97
LINK O3B ADP A 801 MG MG A 803 1555 1555 2.28
LINK O2B ADP B 801 MG MG B 803 1555 1555 2.10
SITE 1 AC1 13 GLN A 206 GLN A 211 SER A 229 GLY A 231
SITE 2 AC1 13 THR A 232 GLY A 233 LYS A 234 SER A 235
SITE 3 AC1 13 TYR A 236 TRP A 380 ARG A 381 ALF A 802
SITE 4 AC1 13 MG A 803
SITE 1 AC2 10 ALA A 230 LYS A 234 GLU A 307 GLN A 346
SITE 2 AC2 10 ARG A 381 GLY A 559 MET A 560 ARG A 584
SITE 3 AC2 10 ADP A 801 MG A 803
SITE 1 AC3 6 SER A 235 ASP A 306 GLU A 307 GLY A 559
SITE 2 AC3 6 ADP A 801 ALF A 802
SITE 1 AC4 13 GLN B 206 GLN B 211 SER B 229 GLY B 231
SITE 2 AC4 13 THR B 232 GLY B 233 LYS B 234 SER B 235
SITE 3 AC4 13 TYR B 236 TRP B 380 ARG B 381 ALF B 802
SITE 4 AC4 13 MG B 803
SITE 1 AC5 12 ALA B 230 GLY B 231 LYS B 234 SER B 235
SITE 2 AC5 12 GLU B 307 GLN B 346 ARG B 381 GLY B 559
SITE 3 AC5 12 MET B 560 ARG B 584 ADP B 801 MG B 803
SITE 1 AC6 6 SER B 235 ASP B 306 GLU B 307 GLY B 559
SITE 2 AC6 6 ADP B 801 ALF B 802
CRYST1 209.850 209.850 78.885 90.00 90.00 120.00 P 32 2 1 12
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.004765 0.002751 0.000000 0.00000
SCALE2 0.000000 0.005503 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012677 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
