HEADER TRANSFERASE 30-AUG-18 6AK5
TITLE BINARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH MNGTP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: POL MU,TERMINAL TRANSFERASE;
COMPND 5 EC: 2.7.7.7,2.7.7.7;
COMPND 6 ENGINEERED: YES;
COMPND 7 OTHER_DETAILS: DELETIONS 398-410
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: POLM, POLMU;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS DNA POLYMERASE MU, DNA BREAK REPAIR, TRANSFERASE-RNTP COMPLEX,
KEYWDS 2 TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.K.CHANG,W.J.WU,M.D.TSAI
REVDAT 3 27-MAR-24 6AK5 1 REMARK LINK
REVDAT 2 12-JUN-19 6AK5 1 JRNL
REVDAT 1 29-MAY-19 6AK5 0
JRNL AUTH Y.K.CHANG,Y.P.HUANG,X.X.LIU,T.P.KO,Y.BESSHO,Y.KAWANO,
JRNL AUTH 2 M.MAESTRE-REYNA,W.J.WU,M.D.TSAI
JRNL TITL HUMAN DNA POLYMERASE MU CAN USE A NONCANONICAL MECHANISM FOR
JRNL TITL 2 MULTIPLE MN2+-MEDIATED FUNCTIONS.
JRNL REF J.AM.CHEM.SOC. V. 141 8489 2019
JRNL REFN ESSN 1520-5126
JRNL PMID 31067051
JRNL DOI 10.1021/JACS.9B01741
REMARK 2
REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0155
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 3 NUMBER OF REFLECTIONS : 41690
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) : 0.210
REMARK 3 R VALUE (WORKING SET) : 0.208
REMARK 3 FREE R VALUE : 0.248
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 2167
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) : 1.70
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2758
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.43
REMARK 3 BIN R VALUE (WORKING SET) : 0.2560
REMARK 3 BIN FREE R VALUE SET COUNT : 136
REMARK 3 BIN FREE R VALUE : 0.2990
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2588
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 69
REMARK 3 SOLVENT ATOMS : 346
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.25
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.02000
REMARK 3 B22 (A**2) : -0.02000
REMARK 3 B33 (A**2) : 0.03000
REMARK 3 B12 (A**2) : 0.00000
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): 0.119
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.630
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2856 ; 0.009 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 2617 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3907 ; 1.428 ; 1.975
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6010 ; 0.921 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 361 ; 5.274 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;35.473 ;23.233
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 457 ;12.040 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;19.659 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.080 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3307 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 701 ; 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): 1402 ; 0.621 ; 1.027
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1401 ; 0.621 ; 1.027
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1774 ; 1.132 ; 1.530
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1775 ; 1.132 ; 1.530
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1454 ; 0.634 ; 1.219
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1414 ; 0.575 ; 1.117
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2071 ; 1.028 ; 1.661
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3295 ; 5.109 ;13.579
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3188 ; 4.736 ;12.791
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 : 1
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 4
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 138 A 229
REMARK 3 RESIDUE RANGE : A 230 A 290
REMARK 3 RESIDUE RANGE : A 291 A 424
REMARK 3 RESIDUE RANGE : A 425 A 494
REMARK 3 ORIGIN FOR THE GROUP (A): 126.9412 89.2245 50.7208
REMARK 3 T TENSOR
REMARK 3 T11: 0.0241 T22: 0.0686
REMARK 3 T33: 0.0520 T12: 0.0159
REMARK 3 T13: 0.0219 T23: 0.0129
REMARK 3 L TENSOR
REMARK 3 L11: 0.3845 L22: 0.4712
REMARK 3 L33: 0.2563 L12: 0.0567
REMARK 3 L13: 0.0273 L23: -0.1578
REMARK 3 S TENSOR
REMARK 3 S11: 0.0600 S12: -0.0081 S13: 0.1341
REMARK 3 S21: 0.0112 S22: -0.0668 S23: -0.0152
REMARK 3 S31: 0.0381 S32: -0.0031 S33: 0.0067
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
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 6AK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-SEP-18.
REMARK 100 THE DEPOSITION ID IS D_1300008914.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-APR-18
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSRRC
REMARK 200 BEAMLINE : TPS 05A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44337
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 13.90
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 45.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 12.30
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.08
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 1.5 M LI2SO4,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
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 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.24350
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 62.45900
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 62.45900
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.62175
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 62.45900
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 62.45900
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.86525
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 62.45900
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.45900
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.62175
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 62.45900
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.45900
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.86525
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 25.24350
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 746 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 903 LIES ON A SPECIAL POSITION.
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 GLY A 127
REMARK 465 SER A 128
REMARK 465 ALA A 129
REMARK 465 ALA A 130
REMARK 465 ALA A 131
REMARK 465 PRO A 132
REMARK 465 LEU A 133
REMARK 465 SER A 134
REMARK 465 PRO A 135
REMARK 465 ALA A 136
REMARK 465 SER A 368
REMARK 465 CYS A 369
REMARK 465 CYS A 370
REMARK 465 GLU A 371
REMARK 465 SER A 372
REMARK 465 PRO A 373
REMARK 465 THR A 374
REMARK 465 ARG A 375
REMARK 465 LEU A 376
REMARK 465 ALA A 377
REMARK 465 GLN A 378
REMARK 465 GLN A 379
REMARK 465 SER A 380
REMARK 465 HIS A 381
REMARK 465 MET A 382
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 175 NE CZ NH1 NH2
REMARK 470 LEU A 196 CG CD1 CD2
REMARK 470 LEU A 199 CG CD1 CD2
REMARK 470 GLN A 200 CG CD OE1 NE2
REMARK 470 GLU A 207 CG CD OE1 OE2
REMARK 470 ARG A 211 CD NE CZ NH1 NH2
REMARK 470 ARG A 230 CD NE CZ NH1 NH2
REMARK 470 LYS A 249 CD CE NZ
REMARK 470 GLN A 308 CD OE1 NE2
REMARK 470 HIS A 367 CG ND1 CD2 CE1 NE2
REMARK 470 ASP A 383 CG OD1 OD2
REMARK 470 LYS A 438 CD CE NZ
REMARK 470 LYS A 450 CE NZ
REMARK 470 GLU A 465 CG CD OE1 OE2
REMARK 470 LYS A 467 CD CE NZ
REMARK 470 ARG A 480 NE CZ NH1 NH2
REMARK 470 GLU A 485 CG CD OE1 OE2
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 ASN A 153 40.31 -145.29
REMARK 500 GLN A 200 43.09 -148.93
REMARK 500 LEU A 202 140.90 -30.87
REMARK 500 ARG A 260 -32.08 -131.90
REMARK 500 THR A 318 -156.55 -126.34
REMARK 500 THR A 318 -151.97 -115.36
REMARK 500 SER A 411 -160.02 -165.70
REMARK 500 ASN A 493 47.74 -88.94
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 MN A 501 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 330 OD1
REMARK 620 2 ASP A 332 OD2 97.2
REMARK 620 3 GTP A 503 O1A 98.3 91.6
REMARK 620 4 GTP A 503 O3G 85.4 174.3 93.0
REMARK 620 5 GTP A 503 O1B 166.2 96.4 83.4 80.9
REMARK 620 6 HOH A 748 O 89.5 91.3 171.3 83.7 88.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 502 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 330 OD2
REMARK 620 2 ASP A 332 OD1 98.5
REMARK 620 3 ASP A 418 OD2 88.3 95.6
REMARK 620 4 GTP A 503 O1A 88.5 89.5 174.3
REMARK 620 5 HOH A 845 O 85.1 170.8 93.0 82.1
REMARK 620 6 HOH A 856 O 150.8 109.9 95.4 85.2 65.8
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 508
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 509
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 510
DBREF 6AK5 A 132 397 UNP Q9NP87 DPOLM_HUMAN 132 397
DBREF 6AK5 A 411 494 UNP Q9NP87 DPOLM_HUMAN 411 494
SEQADV 6AK5 GLY A 127 UNP Q9NP87 EXPRESSION TAG
SEQADV 6AK5 SER A 128 UNP Q9NP87 EXPRESSION TAG
SEQADV 6AK5 ALA A 129 UNP Q9NP87 EXPRESSION TAG
SEQADV 6AK5 ALA A 130 UNP Q9NP87 EXPRESSION TAG
SEQADV 6AK5 ALA A 131 UNP Q9NP87 EXPRESSION TAG
SEQADV 6AK5 GLY A 410 UNP Q9NP87 LINKER
SEQRES 1 A 356 GLY SER ALA ALA ALA PRO LEU SER PRO ALA TRP MET PRO
SEQRES 2 A 356 ALA TYR ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS
SEQRES 3 A 356 ASN THR GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU
SEQRES 4 A 356 ALA ALA GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR
SEQRES 5 A 356 PHE CYS ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER
SEQRES 6 A 356 PRO VAL THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS
SEQRES 7 A 356 PHE GLY GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU
SEQRES 8 A 356 GLU HIS GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG
SEQRES 9 A 356 SER GLU ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE
SEQRES 10 A 356 PHE GLY VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG
SEQRES 11 A 356 GLU GLY LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO
SEQRES 12 A 356 GLN LYS LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS
SEQRES 13 A 356 HIS GLN ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL
SEQRES 14 A 356 ASP ALA LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN
SEQRES 15 A 356 ALA LEU PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE
SEQRES 16 A 356 ARG ARG GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU
SEQRES 17 A 356 ILE THR HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU
SEQRES 18 A 356 PRO ARG VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE
SEQRES 19 A 356 LEU TYR HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO
SEQRES 20 A 356 THR ARG LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU
SEQRES 21 A 356 ARG SER PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER
SEQRES 22 A 356 TRP LYS ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL
SEQRES 23 A 356 SER GLN PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER
SEQRES 24 A 356 LYS LEU PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS
SEQRES 25 A 356 GLU LYS GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP
SEQRES 26 A 356 PRO GLU GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU
SEQRES 27 A 356 ASP ILE PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO
SEQRES 28 A 356 GLU GLN ARG ASN ALA
HET MN A 501 1
HET MN A 502 1
HET GTP A 503 32
HET SO4 A 504 5
HET SO4 A 505 5
HET SO4 A 506 5
HET SO4 A 507 5
HET SO4 A 508 5
HET SO4 A 509 5
HET SO4 A 510 5
HETNAM MN MANGANESE (II) ION
HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE
HETNAM SO4 SULFATE ION
FORMUL 2 MN 2(MN 2+)
FORMUL 4 GTP C10 H16 N5 O14 P3
FORMUL 5 SO4 7(O4 S 2-)
FORMUL 12 HOH *346(H2 O)
HELIX 1 AA1 TYR A 141 ARG A 145 5 5
HELIX 2 AA2 ASN A 153 GLU A 170 1 18
HELIX 3 AA3 SER A 172 LEU A 189 1 18
HELIX 4 AA4 THR A 195 LEU A 199 5 5
HELIX 5 AA5 GLY A 206 GLY A 220 1 15
HELIX 6 AA6 CYS A 222 SER A 231 1 10
HELIX 7 AA7 SER A 231 ILE A 243 1 13
HELIX 8 AA8 GLY A 247 GLU A 257 1 11
HELIX 9 AA9 THR A 261 GLU A 267 1 7
HELIX 10 AB1 GLN A 268 LEU A 272 5 5
HELIX 11 AB2 THR A 273 HIS A 282 1 10
HELIX 12 AB3 HIS A 282 SER A 287 1 6
HELIX 13 AB4 ARG A 292 LEU A 310 1 19
HELIX 14 AB5 THR A 318 ARG A 323 1 6
HELIX 15 AB6 GLY A 345 GLN A 357 1 13
HELIX 16 AB7 PRO A 423 SER A 425 5 3
HELIX 17 AB8 GLN A 426 GLY A 436 1 11
HELIX 18 AB9 SER A 437 GLY A 453 1 17
HELIX 19 AC1 SER A 474 LEU A 482 1 9
HELIX 20 AC2 PRO A 488 ARG A 492 5 5
SHEET 1 AA1 2 VAL A 290 LEU A 291 0
SHEET 2 AA1 2 GLN A 327 GLY A 328 -1 O GLY A 328 N VAL A 290
SHEET 1 AA2 5 THR A 314 LEU A 317 0
SHEET 2 AA2 5 VAL A 331 THR A 336 -1 O THR A 336 N THR A 314
SHEET 3 AA2 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335
SHEET 4 AA2 5 GLU A 386 GLN A 396 -1 N PHE A 392 O VAL A 415
SHEET 5 AA2 5 ILE A 360 GLN A 366 -1 N LEU A 361 O ILE A 391
SHEET 1 AA3 3 TRP A 455 LEU A 456 0
SHEET 2 AA3 3 LEU A 461 ASP A 463 -1 O PHE A 462 N TRP A 455
SHEET 3 AA3 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463
LINK OD1 ASP A 330 MN MN A 501 1555 1555 2.05
LINK OD2 ASP A 330 MN MN A 502 1555 1555 2.08
LINK OD2 ASP A 332 MN MN A 501 1555 1555 2.12
LINK OD1 ASP A 332 MN MN A 502 1555 1555 2.17
LINK OD2 ASP A 418 MN MN A 502 1555 1555 2.26
LINK MN MN A 501 O1A GTP A 503 1555 1555 2.02
LINK MN MN A 501 O3G GTP A 503 1555 1555 2.16
LINK MN MN A 501 O1B GTP A 503 1555 1555 2.15
LINK MN MN A 501 O HOH A 748 1555 1555 2.32
LINK MN MN A 502 O1A GTP A 503 1555 1555 2.79
LINK MN MN A 502 O HOH A 845 1555 1555 2.46
LINK MN MN A 502 O HOH A 856 1555 1555 1.91
CISPEP 1 GLY A 436 SER A 437 0 -3.05
SITE 1 AC1 4 ASP A 330 ASP A 332 GTP A 503 HOH A 748
SITE 1 AC2 6 ASP A 330 ASP A 332 ASP A 418 GTP A 503
SITE 2 AC2 6 HOH A 845 HOH A 856
SITE 1 AC3 22 GLY A 319 GLY A 320 ARG A 323 LYS A 325
SITE 2 AC3 22 GLY A 328 HIS A 329 ASP A 330 ASP A 332
SITE 3 AC3 22 ARG A 387 GLY A 433 TRP A 434 GLY A 436
SITE 4 AC3 22 SER A 458 MN A 501 MN A 502 SO4 A 508
SITE 5 AC3 22 HOH A 602 HOH A 631 HOH A 653 HOH A 736
SITE 6 AC3 22 HOH A 748 HOH A 762
SITE 1 AC4 5 GLY A 247 LYS A 249 THR A 250 HOH A 633
SITE 2 AC4 5 HOH A 854
SITE 1 AC5 4 SER A 172 GLU A 173 GLY A 174 ARG A 175
SITE 1 AC6 5 ARG A 229 THR A 273 GLN A 274 HOH A 637
SITE 2 AC6 5 HOH A 674
SITE 1 AC7 3 ARG A 446 ARG A 449 LYS A 450
SITE 1 AC8 5 ARG A 445 ASN A 457 SER A 458 HIS A 459
SITE 2 AC8 5 GTP A 503
SITE 1 AC9 7 HIS A 329 ARG A 416 HOH A 619 HOH A 653
SITE 2 AC9 7 HOH A 725 HOH A 823 HOH A 845
SITE 1 AD1 4 ARG A 253 ARG A 256 HOH A 629 HOH A 737
CRYST1 124.918 124.918 50.487 90.00 90.00 90.00 P 41 21 2 8
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 0.008005 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008005 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019807 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
