HEADER TRANSFERASE/DNA 27-AUG-13 4MFF
TITLE STRUCTURE OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH O6MG IN THE
TITLE 2 TEMPLATE BASE PAIRED WITH INCOMING NON-HYDROLYZABLE TTP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE BETA;
COMPND 3 CHAIN: A;
COMPND 4 EC: 2.7.7.7, 4.2.99.-;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: TEMPLATE;
COMPND 8 CHAIN: T;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 3;
COMPND 11 MOLECULE: UP PRIMER;
COMPND 12 CHAIN: P;
COMPND 13 ENGINEERED: YES;
COMPND 14 MOL_ID: 4;
COMPND 15 MOLECULE: DN PRIMER;
COMPND 16 CHAIN: D;
COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: POLB;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 OTHER_DETAILS: SYNTHETIC TEMPLATE;
SOURCE 11 MOL_ID: 3;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 OTHER_DETAILS: SYNTHETIC UP PRIMER;
SOURCE 14 MOL_ID: 4;
SOURCE 15 SYNTHETIC: YES;
SOURCE 16 OTHER_DETAILS: SYNTHETIC DN PRIMER
KEYWDS DNA POLYMERASE X FAMILY, DNA SYNTHESIS, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.C.KOAG,K.MIN,A.F.MONZINGO,S.LEE
REVDAT 3 28-FEB-24 4MFF 1 REMARK LINK
REVDAT 2 02-JUL-14 4MFF 1 JRNL
REVDAT 1 16-APR-14 4MFF 0
JRNL AUTH M.C.KOAG,S.LEE
JRNL TITL METAL-DEPENDENT CONFORMATIONAL ACTIVATION EXPLAINS HIGHLY
JRNL TITL 2 PROMUTAGENIC REPLICATION ACROSS O6-METHYLGUANINE BY HUMAN
JRNL TITL 3 DNA POLYMERASE BETA.
JRNL REF J.AM.CHEM.SOC. V. 136 5709 2014
JRNL REFN ISSN 0002-7863
JRNL PMID 24694247
JRNL DOI 10.1021/JA500172D
REMARK 2
REMARK 2 RESOLUTION. 2.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.6.0117
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) : 2.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2
REMARK 3 NUMBER OF REFLECTIONS : 13877
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) : 0.226
REMARK 3 R VALUE (WORKING SET) : 0.222
REMARK 3 FREE R VALUE : 0.294
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 695
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) : 2.55
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62
REMARK 3 REFLECTION IN BIN (WORKING SET) : 866
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.90
REMARK 3 BIN R VALUE (WORKING SET) : 0.3360
REMARK 3 BIN FREE R VALUE SET COUNT : 42
REMARK 3 BIN FREE R VALUE : 0.3630
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2559
REMARK 3 NUCLEIC ACID ATOMS : 633
REMARK 3 HETEROGEN ATOMS : 33
REMARK 3 SOLVENT ATOMS : 51
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.28
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.44000
REMARK 3 B22 (A**2) : -0.04000
REMARK 3 B33 (A**2) : -0.14000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.47000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 4.417
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.388
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.273
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.781
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.899
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.816
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3350 ; 0.011 ; 0.018
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4646 ; 1.617 ; 1.852
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 320 ; 6.015 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;36.613 ;24.000
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;18.357 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.987 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 483 ; 0.100 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2281 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; 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 : 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 USED IF PRESENT IN
REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY
REMARK 4
REMARK 4 4MFF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-13.
REMARK 100 THE DEPOSITION ID IS D_1000081842.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-JUN-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14547
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.40
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 14% - 23% PEG3400, AND 350 MM SODIUM
REMARK 280 ACETATE , PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
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 39.41950
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4750 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21120 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D
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 THR A 205
REMARK 465 LYS A 206
REMARK 465 GLN A 207
REMARK 465 ASN A 245
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 GLU A 203 CG CD OE1 OE2
REMARK 470 LYS A 244 CG CD CE NZ
REMARK 470 ASP A 246 CG OD1 OD2
REMARK 470 GLU A 247 CG CD OE1 OE2
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 CD LYS A 27 O HOH A 504 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 MG MG A 402 O HOH A 510 1655 1.68
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 HIS A 34 CG HIS A 34 CD2 0.060
REMARK 500 HIS A 135 CG HIS A 135 CD2 0.059
REMARK 500 HIS A 212 CG HIS A 212 CD2 0.056
REMARK 500 DG D 1 P DG D 1 OP3 -0.108
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 6OG T 6 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES
REMARK 500 DT T 12 O5' - P - OP1 ANGL. DEV. = -5.8 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 PRO A 50 43.68 -91.76
REMARK 500 GLU A 129 -34.73 -34.17
REMARK 500 LYS A 141 -47.42 -29.44
REMARK 500 ASP A 170 116.81 -170.26
REMARK 500 CYS A 178 -143.15 -100.60
REMARK 500 GLU A 247 154.76 -39.82
REMARK 500 ASN A 294 -166.00 -114.35
REMARK 500 LYS A 317 -36.82 -38.49
REMARK 500 ASP A 321 -72.32 -56.84
REMARK 500 TYR A 322 -49.00 -18.14
REMARK 500 ARG A 333 30.35 -99.87
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 NA D 101 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 60 O
REMARK 620 2 VAL A 65 O 70.1
REMARK 620 3 DC D 3 OP1 123.3 79.5
REMARK 620 4 DC D 3 OP2 153.2 83.2 51.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 403 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 101 O
REMARK 620 2 VAL A 103 O 92.3
REMARK 620 3 ILE A 106 O 104.1 91.4
REMARK 620 4 DG P 9 OP1 152.0 102.8 99.0
REMARK 620 5 HOH P 101 O 86.2 93.9 168.3 69.6
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 401 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD1
REMARK 620 2 1FZ A 404 O2B 175.4
REMARK 620 3 1FZ A 404 O1G 94.7 82.6
REMARK 620 4 1FZ A 404 O1A 100.1 75.7 78.0
REMARK 620 5 HOH A 538 O 80.7 100.4 159.2 82.8
REMARK 620 6 HOH A 539 O 102.3 80.9 77.4 147.9 123.4
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 MG A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1FZ A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 101
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3ISB RELATED DB: PDB
REMARK 900 RELATED ID: 1BPX RELATED DB: PDB
REMARK 900 RELATED ID: 4MF2 RELATED DB: PDB
REMARK 900 RELATED ID: 4MF8 RELATED DB: PDB
REMARK 900 RELATED ID: 4MFA RELATED DB: PDB
REMARK 900 RELATED ID: 4MFC RELATED DB: PDB
DBREF 4MFF A 11 335 UNP P06746 DPOLB_HUMAN 11 335
DBREF 4MFF T 1 16 PDB 4MFF 4MFF 1 16
DBREF 4MFF P 1 10 PDB 4MFF 4MFF 1 10
DBREF 4MFF D 1 5 PDB 4MFF 4MFF 1 5
SEQRES 1 A 325 LEU ASN GLY GLY ILE THR ASP MET LEU THR GLU LEU ALA
SEQRES 2 A 325 ASN PHE GLU LYS ASN VAL SER GLN ALA ILE HIS LYS TYR
SEQRES 3 A 325 ASN ALA TYR ARG LYS ALA ALA SER VAL ILE ALA LYS TYR
SEQRES 4 A 325 PRO HIS LYS ILE LYS SER GLY ALA GLU ALA LYS LYS LEU
SEQRES 5 A 325 PRO GLY VAL GLY THR LYS ILE ALA GLU LYS ILE ASP GLU
SEQRES 6 A 325 PHE LEU ALA THR GLY LYS LEU ARG LYS LEU GLU LYS ILE
SEQRES 7 A 325 ARG GLN ASP ASP THR SER SER SER ILE ASN PHE LEU THR
SEQRES 8 A 325 ARG VAL SER GLY ILE GLY PRO SER ALA ALA ARG LYS PHE
SEQRES 9 A 325 VAL ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG LYS
SEQRES 10 A 325 ASN GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU
SEQRES 11 A 325 LYS TYR PHE GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU
SEQRES 12 A 325 GLU MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU VAL
SEQRES 13 A 325 LYS LYS VAL ASP SER GLU TYR ILE ALA THR VAL CYS GLY
SEQRES 14 A 325 SER PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET ASP
SEQRES 15 A 325 VAL LEU LEU THR HIS PRO SER PHE THR SER GLU SER THR
SEQRES 16 A 325 LYS GLN PRO LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU
SEQRES 17 A 325 GLN LYS VAL HIS PHE ILE THR ASP THR LEU SER LYS GLY
SEQRES 18 A 325 GLU THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER LYS
SEQRES 19 A 325 ASN ASP GLU LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE
SEQRES 20 A 325 ARG LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU
SEQRES 21 A 325 TYR PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET ARG
SEQRES 22 A 325 ALA HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU TYR
SEQRES 23 A 325 THR ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY GLU
SEQRES 24 A 325 PRO LEU PRO VAL ASP SER GLU LYS ASP ILE PHE ASP TYR
SEQRES 25 A 325 ILE GLN TRP LYS TYR ARG GLU PRO LYS ASP ARG SER GLU
SEQRES 1 T 16 DC DC DG DA DC 6OG DT DC DG DC DA DT DC
SEQRES 2 T 16 DA DG DC
SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DA
SEQRES 1 D 5 DG DT DC DG DG
MODRES 4MFF 6OG T 6 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
HET 6OG T 6 23
HET MG A 401 1
HET MG A 402 1
HET NA A 403 1
HET 1FZ A 404 29
HET NA D 101 1
HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE
HETNAM MG MAGNESIUM ION
HETNAM NA SODIUM ION
HETNAM 1FZ 5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 1FZ PHOSPHORYL]AMINO}PHOSPHORYL]THYMIDINE
FORMUL 2 6OG C11 H16 N5 O7 P
FORMUL 5 MG 2(MG 2+)
FORMUL 7 NA 2(NA 1+)
FORMUL 8 1FZ C10 H18 N3 O13 P3
FORMUL 10 HOH *51(H2 O)
HELIX 1 1 ASN A 12 VAL A 29 1 18
HELIX 2 2 ALA A 32 LYS A 48 1 17
HELIX 3 3 SER A 55 LYS A 60 1 6
HELIX 4 4 GLY A 66 GLY A 80 1 15
HELIX 5 5 LEU A 82 GLN A 90 1 9
HELIX 6 6 ASP A 91 THR A 101 1 11
HELIX 7 7 GLY A 107 GLU A 117 1 11
HELIX 8 8 THR A 121 LYS A 127 1 7
HELIX 9 9 ASN A 128 LEU A 132 5 5
HELIX 10 10 ASN A 133 TYR A 142 1 10
HELIX 11 11 GLY A 144 LYS A 148 5 5
HELIX 12 12 ARG A 152 ASP A 170 1 19
HELIX 13 13 CYS A 178 GLY A 184 1 7
HELIX 14 14 LEU A 211 VAL A 221 1 11
HELIX 15 15 PRO A 261 PHE A 272 1 12
HELIX 16 16 SER A 275 LYS A 289 1 15
HELIX 17 17 SER A 315 ILE A 323 1 9
HELIX 18 18 GLU A 329 ARG A 333 5 5
SHEET 1 A 2 ILE A 150 PRO A 151 0
SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150
SHEET 1 B 5 ILE A 174 VAL A 177 0
SHEET 2 B 5 MET A 191 THR A 196 -1 O THR A 196 N ILE A 174
SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195
SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253
SHEET 5 B 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236
SHEET 1 C 2 PHE A 291 ILE A 293 0
SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292
LINK O3' DC T 5 P 6OG T 6 1555 1555 1.61
LINK O3' 6OG T 6 P DT T 7 1555 1555 1.60
LINK O SER A 30 MG MG A 402 1555 1555 2.42
LINK O LYS A 60 NA NA D 101 1555 1555 2.68
LINK O VAL A 65 NA NA D 101 1555 1555 2.88
LINK O THR A 101 NA NA A 403 1555 1555 2.31
LINK O VAL A 103 NA NA A 403 1555 1555 2.35
LINK O ILE A 106 NA NA A 403 1555 1555 2.02
LINK OD1 ASP A 190 MG MG A 401 1555 1555 2.14
LINK MG MG A 401 O2B 1FZ A 404 1555 1555 2.05
LINK MG MG A 401 O1G 1FZ A 404 1555 1555 2.27
LINK MG MG A 401 O1A 1FZ A 404 1555 1555 2.35
LINK MG MG A 401 O HOH A 538 1555 1555 2.44
LINK MG MG A 401 O HOH A 539 1555 1555 2.32
LINK NA NA A 403 OP1 DG P 9 1555 1555 2.42
LINK NA NA A 403 O HOH P 101 1555 1555 3.02
LINK OP1 DC D 3 NA NA D 101 1555 1555 2.90
LINK OP2 DC D 3 NA NA D 101 1555 1555 3.04
CISPEP 1 GLY A 274 SER A 275 0 -3.11
SITE 1 AC1 4 ASP A 190 1FZ A 404 HOH A 538 HOH A 539
SITE 1 AC2 4 SER A 30 GLN A 31 SER A 171 HOH A 510
SITE 1 AC3 5 THR A 101 VAL A 103 ILE A 106 DG P 9
SITE 2 AC3 5 HOH P 101
SITE 1 AC4 16 ARG A 149 GLY A 179 SER A 180 ARG A 183
SITE 2 AC4 16 SER A 188 GLY A 189 ASP A 190 TYR A 271
SITE 3 AC4 16 PHE A 272 THR A 273 GLY A 274 ASP A 276
SITE 4 AC4 16 ASN A 279 MG A 401 HOH A 539 DA P 10
SITE 1 AC5 3 LYS A 60 VAL A 65 DC D 3
CRYST1 54.546 78.839 54.751 90.00 105.95 90.00 P 1 21 1 2
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 0.018333 0.000000 0.005239 0.00000
SCALE2 0.000000 0.012684 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018996 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
