HEADER TRANSFERASE/DNA 16-MAR-18 6CRB
TITLE TERNARY COMPLEX CRYSTAL STRUCTURE OF DNA POLYMERASE BETA WITH A
TITLE 2 DIDEOXY TERMINATED PRIMER WITH CF2, BETA, GAMMA DATP ANALOGUE
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 STRAND;
COMPND 8 CHAIN: T;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 3;
COMPND 11 MOLECULE: PRIMER STRAND;
COMPND 12 CHAIN: P;
COMPND 13 ENGINEERED: YES;
COMPND 14 MOL_ID: 4;
COMPND 15 MOLECULE: DOWNSTREAM PRIMER STRAND;
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 EXPRESSION_SYSTEM_STRAIN: TAP56;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PWL-11;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 14 ORGANISM_TAXID: 9606;
SOURCE 15 MOL_ID: 3;
SOURCE 16 SYNTHETIC: YES;
SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 18 ORGANISM_TAXID: 9606;
SOURCE 19 MOL_ID: 4;
SOURCE 20 SYNTHETIC: YES;
SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 22 ORGANISM_TAXID: 9606
KEYWDS CONFORMATIONAL CHANGE, ENZYME MECHANISM, LFER, TRANSFERASE-DNA
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR V.K.BATRA,S.H.WILSON
REVDAT 2 04-OCT-23 6CRB 1 LINK
REVDAT 1 18-JUL-18 6CRB 0
JRNL AUTH V.K.BATRA,K.OERTELL,W.A.BEARD,B.A.KASHEMIROV,C.E.MCKENNA,
JRNL AUTH 2 M.F.GOODMAN,S.H.WILSON
JRNL TITL MAPPING FUNCTIONAL SUBSTRATE-ENZYME INTERACTIONS IN THE POL
JRNL TITL 2 BETA ACTIVE SITE THROUGH CHEMICAL BIOLOGY: STRUCTURAL
JRNL TITL 3 RESPONSES TO ACIDITY MODIFICATION OF INCOMING DNTPS.
JRNL REF BIOCHEMISTRY V. 57 3934 2018
JRNL REFN ISSN 1520-4995
JRNL PMID 29874056
JRNL DOI 10.1021/ACS.BIOCHEM.8B00418
REMARK 2
REMARK 2 RESOLUTION. 2.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.97
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9
REMARK 3 NUMBER OF REFLECTIONS : 22653
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.223
REMARK 3 R VALUE (WORKING SET) : 0.218
REMARK 3 FREE R VALUE : 0.275
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.850
REMARK 3 FREE R VALUE TEST SET COUNT : 2004
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 19.9739 - 5.1570 1.00 1592 157 0.1701 0.1945
REMARK 3 2 5.1570 - 4.1050 1.00 1561 153 0.1814 0.2173
REMARK 3 3 4.1050 - 3.5895 0.99 1549 154 0.1877 0.2622
REMARK 3 4 3.5895 - 3.2628 1.00 1549 150 0.1955 0.2659
REMARK 3 5 3.2628 - 3.0298 1.00 1536 148 0.2417 0.2854
REMARK 3 6 3.0298 - 2.8517 1.00 1567 149 0.2786 0.3991
REMARK 3 7 2.8517 - 2.7093 0.99 1533 154 0.2804 0.3423
REMARK 3 8 2.7093 - 2.5916 0.99 1520 143 0.2757 0.3414
REMARK 3 9 2.5916 - 2.4920 0.99 1543 147 0.2660 0.3269
REMARK 3 10 2.4920 - 2.4062 0.97 1507 148 0.2794 0.3816
REMARK 3 11 2.4062 - 2.3311 0.93 1444 140 0.2630 0.3285
REMARK 3 12 2.3311 - 2.2645 0.87 1342 126 0.2657 0.3234
REMARK 3 13 2.2645 - 2.2050 0.82 1267 124 0.2585 0.3210
REMARK 3 14 2.2050 - 2.1512 0.73 1139 111 0.2773 0.3474
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.260
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.34
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.009 3387
REMARK 3 ANGLE : 1.269 4698
REMARK 3 CHIRALITY : 0.062 513
REMARK 3 PLANARITY : 0.006 494
REMARK 3 DIHEDRAL : 20.941 1321
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6CRB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-18.
REMARK 100 THE DEPOSITION ID IS D_1000233071.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-APR-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5, 50 MM IMIDAZOLE, 350 MM
REMARK 200 SODIUM ACETATE
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
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 : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22684
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.07400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19
REMARK 200 COMPLETENESS FOR SHELL (%) : 72.3
REMARK 200 DATA REDUNDANCY IN SHELL : 2.70
REMARK 200 R MERGE FOR SHELL (I) : 0.45700
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: PHENIX
REMARK 200 STARTING MODEL: 2FMS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.34
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 16-18% PEG 3350, VAPOR DIFFUSION,
REMARK 280 SITTING DROP, TEMPERATURE 291K
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 39.38600
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: 5110 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20390 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 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 MET A 1
REMARK 465 SER A 2
REMARK 465 LYS A 3
REMARK 465 ARG A 4
REMARK 465 LYS A 5
REMARK 465 ALA A 6
REMARK 465 THR A 205
REMARK 465 LYS A 206
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 GLN A 8 CG CD OE1 NE2
REMARK 470 GLU A 9 CG CD OE1 OE2
REMARK 470 GLU A 203 CG CD OE1 OE2
REMARK 470 ASN A 245 CG OD1 ND2
REMARK 470 LYS A 289 CG CD CE NZ
REMARK 470 VAL A 303 CG1 CG2
REMARK 470 DG P 1 O6
REMARK 470 DC P 10 O3'
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 ND1 HIS A 34 O HOH A 501 1.89
REMARK 500 OP2 DA T 14 O HOH T 101 1.90
REMARK 500 OP1 DA T 11 O HOH T 102 1.94
REMARK 500 OP1 DC P 10 O HOH P 101 1.97
REMARK 500 O PRO A 63 O HOH A 502 1.99
REMARK 500 O HOH T 118 O HOH T 121 2.01
REMARK 500 N7 DG T 15 O HOH T 103 2.03
REMARK 500 O HOH A 607 O HOH A 625 2.03
REMARK 500 O HOH A 576 O HOH A 623 2.04
REMARK 500 OP1 DG D 1 O HOH D 101 2.06
REMARK 500 O HOH D 106 O HOH D 109 2.09
REMARK 500 O HOH A 529 O HOH A 616 2.10
REMARK 500 O HOH A 615 O HOH A 616 2.12
REMARK 500 O HOH A 569 O HOH A 618 2.13
REMARK 500 OE2 GLU A 165 O HOH A 503 2.15
REMARK 500 OD1 ASN A 28 O HOH A 504 2.15
REMARK 500 OD1 ASN A 37 O HOH A 505 2.15
REMARK 500 O PRO A 312 N ASP A 314 2.15
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 DG P 9 O3' DG P 9 C3' -0.045
REMARK 500 DG D 1 P DG D 1 OP3 -0.115
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 DG T 15 O4' - C1' - N9 ANGL. DEV. = 2.8 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 GLU A 9 -55.04 71.97
REMARK 500 PRO A 50 34.05 -87.88
REMARK 500 ASP A 170 112.57 -172.43
REMARK 500 CYS A 178 -141.87 -104.30
REMARK 500 SER A 199 38.44 -95.43
REMARK 500 THR A 201 -38.23 -154.55
REMARK 500 SER A 202 -23.10 -171.99
REMARK 500 GLU A 203 -88.02 -80.43
REMARK 500 PRO A 208 63.69 -52.57
REMARK 500 LYS A 209 3.09 -151.07
REMARK 500 LYS A 244 -114.72 -100.16
REMARK 500 ASN A 245 -98.70 -70.17
REMARK 500 VAL A 303 -96.09 -70.37
REMARK 500 THR A 304 41.01 -146.17
REMARK 500 ALA A 307 -103.97 -80.76
REMARK 500 VAL A 313 -11.18 43.57
REMARK 500 ASP A 314 -65.08 17.49
REMARK 500 SER A 315 -145.54 -100.77
REMARK 500 LYS A 317 -53.63 -176.47
REMARK 500 ASP A 318 48.90 6.82
REMARK 500 ASP A 332 43.81 -97.67
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 THR A 273 GLY A 274 -35.23
REMARK 500 LEU A 311 PRO A 312 -132.47
REMARK 500 LYS A 317 ASP A 318 -148.20
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 A 404 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 60 O
REMARK 620 2 LEU A 62 O 90.6
REMARK 620 3 VAL A 65 O 91.7 91.0
REMARK 620 4 HOH A 510 O 95.4 172.6 84.6
REMARK 620 5 HOH A 597 O 100.9 77.2 162.8 105.6
REMARK 620 6 DC D 3 OP1 172.2 86.3 81.3 87.2 85.4
REMARK 620 N 1 2 3 4 5
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 104.4
REMARK 620 3 ILE A 106 O 96.2 84.3
REMARK 620 4 HOH A 611 O 82.0 91.7 175.0
REMARK 620 5 DG P 9 OP1 156.7 96.2 96.5 86.8
REMARK 620 6 HOH P 103 O 74.4 173.5 89.4 94.5 86.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 402 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD1
REMARK 620 2 ASP A 192 OD2 98.0
REMARK 620 3 VA6 A 401 O1A 103.8 91.1
REMARK 620 4 VA6 A 401 O1G 86.1 167.7 99.2
REMARK 620 5 VA6 A 401 O1B 163.2 94.4 87.1 79.5
REMARK 620 6 HOH A 541 O 91.5 90.0 164.3 78.2 77.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 405 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD2
REMARK 620 2 ASP A 192 OD1 96.3
REMARK 620 3 ASP A 256 OD2 110.1 89.8
REMARK 620 4 VA6 A 401 O1A 73.8 82.1 171.4
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue VA6 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 NA A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405
DBREF 6CRB A 1 335 UNP P06746 DPOLB_HUMAN 1 335
DBREF 6CRB T 1 16 PDB 6CRB 6CRB 1 16
DBREF 6CRB P 1 10 PDB 6CRB 6CRB 1 10
DBREF 6CRB D 1 5 PDB 6CRB 6CRB 1 5
SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY
SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU
SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR
SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS
SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL
SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA
SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP
SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER
SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU
SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP
SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE
SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU
SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL
SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG
SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU
SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO
SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL
SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS
SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU
SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE
SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR
SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA
SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG
SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO
SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP
SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU
SEQRES 1 T 16 DC DC DG DA DC DT DG 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 DC
SEQRES 1 D 5 DG DT DC DG DG
HET VA6 A 401 32
HET MG A 402 1
HET NA A 403 1
HET NA A 404 1
HET NA A 405 1
HETNAM VA6 9-{2-DEOXY-5-O-[(S)-{[(S)-[DIFLUORO(PHOSPHONO)
HETNAM 2 VA6 METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]-
HETNAM 3 VA6 ALPHA-D-ERYTHRO-PENTOFURANOSYL}-9H-PURIN-6-AMINE
HETNAM MG MAGNESIUM ION
HETNAM NA SODIUM ION
FORMUL 5 VA6 C11 H16 F2 N5 O11 P3
FORMUL 6 MG MG 2+
FORMUL 7 NA 3(NA 1+)
FORMUL 10 HOH *175(H2 O)
HELIX 1 AA1 ASN A 12 VAL A 29 1 18
HELIX 2 AA2 ALA A 32 TYR A 49 1 18
HELIX 3 AA3 SER A 55 LYS A 61 1 7
HELIX 4 AA4 GLY A 66 GLY A 80 1 15
HELIX 5 AA5 LEU A 82 ASP A 91 1 10
HELIX 6 AA6 ASP A 91 THR A 101 1 11
HELIX 7 AA7 GLY A 107 GLU A 117 1 11
HELIX 8 AA8 THR A 121 LYS A 127 1 7
HELIX 9 AA9 ASN A 128 LEU A 132 5 5
HELIX 10 AB1 ASN A 133 TYR A 142 1 10
HELIX 11 AB2 GLY A 144 LYS A 148 5 5
HELIX 12 AB3 ARG A 152 ASP A 170 1 19
HELIX 13 AB4 CYS A 178 ARG A 183 1 6
HELIX 14 AB5 LYS A 209 VAL A 221 1 13
HELIX 15 AB6 PRO A 261 ASP A 263 5 3
HELIX 16 AB7 GLN A 264 THR A 273 1 10
HELIX 17 AB8 SER A 275 GLY A 290 1 16
HELIX 18 AB9 ASP A 318 ILE A 323 1 6
HELIX 19 AC1 GLU A 329 ARG A 333 5 5
SHEET 1 AA1 2 ILE A 150 PRO A 151 0
SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150
SHEET 1 AA2 5 ILE A 174 VAL A 177 0
SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176
SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195
SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N GLY A 237 O ILE A 255
SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236
SHEET 1 AA3 2 PHE A 291 ILE A 293 0
SHEET 2 AA3 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292
LINK O LYS A 60 NA NA A 404 1555 1555 2.30
LINK O LEU A 62 NA NA A 404 1555 1555 2.59
LINK O VAL A 65 NA NA A 404 1555 1555 2.48
LINK O THR A 101 NA NA A 403 1555 1555 2.25
LINK O VAL A 103 NA NA A 403 1555 1555 2.45
LINK O ILE A 106 NA NA A 403 1555 1555 2.35
LINK OD1 ASP A 190 MG MG A 402 1555 1555 1.85
LINK OD2 ASP A 190 NA NA A 405 1555 1555 2.46
LINK OD2 ASP A 192 MG MG A 402 1555 1555 2.42
LINK OD1 ASP A 192 NA NA A 405 1555 1555 2.52
LINK OD2 ASP A 256 NA NA A 405 1555 1555 2.78
LINK O1A VA6 A 401 MG MG A 402 1555 1555 1.93
LINK O1G VA6 A 401 MG MG A 402 1555 1555 2.19
LINK O1B VA6 A 401 MG MG A 402 1555 1555 2.09
LINK O1A VA6 A 401 NA NA A 405 1555 1555 2.92
LINK MG MG A 402 O HOH A 541 1555 1555 2.11
LINK NA NA A 403 O HOH A 611 1555 1555 2.64
LINK NA NA A 403 OP1 DG P 9 1555 1555 2.36
LINK NA NA A 403 O HOH P 103 1555 1555 2.70
LINK NA NA A 404 O HOH A 510 1555 1555 2.59
LINK NA NA A 404 O HOH A 597 1555 1555 2.85
LINK NA NA A 404 OP1 DC D 3 1555 1555 2.85
CISPEP 1 GLY A 274 SER A 275 0 5.81
SITE 1 AC1 19 ARG A 149 GLY A 179 SER A 180 ARG A 183
SITE 2 AC1 19 SER A 188 GLY A 189 ASP A 190 ASP A 192
SITE 3 AC1 19 TYR A 271 THR A 273 GLY A 274 ASP A 276
SITE 4 AC1 19 MG A 402 NA A 405 HOH A 541 HOH A 567
SITE 5 AC1 19 DC P 10 DT T 6 DG T 7
SITE 1 AC2 4 ASP A 190 ASP A 192 VA6 A 401 HOH A 541
SITE 1 AC3 6 THR A 101 VAL A 103 ILE A 106 HOH A 611
SITE 2 AC3 6 DG P 9 HOH P 103
SITE 1 AC4 6 LYS A 60 LEU A 62 VAL A 65 HOH A 510
SITE 2 AC4 6 HOH A 597 DC D 3
SITE 1 AC5 5 ASP A 190 ASP A 192 ASP A 256 VA6 A 401
SITE 2 AC5 5 DC P 10
CRYST1 54.763 78.772 54.472 90.00 108.78 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 0.018261 0.000000 0.006209 0.00000
SCALE2 0.000000 0.012695 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019390 0.00000