HEADER TRANSFERASE/DNA 16-MAR-18 6CRC
TITLE TERNARY COMPLEX CRYSTAL STRUCTURE OF DNA POLYMERASE BETA WITH A
TITLE 2 DIDEOXY TERMINATED PRIMER WITH CCL2, 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_COMMON: HUMAN;
SOURCE 15 ORGANISM_TAXID: 9606;
SOURCE 16 MOL_ID: 3;
SOURCE 17 SYNTHETIC: YES;
SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 19 ORGANISM_COMMON: HUMAN;
SOURCE 20 ORGANISM_TAXID: 9606;
SOURCE 21 MOL_ID: 4;
SOURCE 22 SYNTHETIC: YES;
SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 24 ORGANISM_COMMON: HUMAN;
SOURCE 25 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 3 30-OCT-24 6CRC 1 REMARK
REVDAT 2 04-OCT-23 6CRC 1 LINK
REVDAT 1 25-JUL-18 6CRC 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. 2.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.10.1_2155
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) : 2.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 84.3
REMARK 3 NUMBER OF REFLECTIONS : 16571
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.214
REMARK 3 R VALUE (WORKING SET) : 0.207
REMARK 3 FREE R VALUE : 0.285
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.880
REMARK 3 FREE R VALUE TEST SET COUNT : 1638
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 19.9803 - 5.2343 1.00 1512 167 0.1544 0.2037
REMARK 3 2 5.2343 - 4.1670 0.97 1437 161 0.1713 0.2348
REMARK 3 3 4.1670 - 3.6439 0.97 1443 158 0.1815 0.2675
REMARK 3 4 3.6439 - 3.3124 0.99 1471 164 0.1908 0.2818
REMARK 3 5 3.3124 - 3.0759 0.96 1391 160 0.2296 0.3264
REMARK 3 6 3.0759 - 2.8951 0.80 1186 125 0.2784 0.3878
REMARK 3 7 2.8951 - 2.7505 0.75 1113 119 0.2758 0.4018
REMARK 3 8 2.7505 - 2.6310 0.76 1116 128 0.2824 0.3376
REMARK 3 9 2.6310 - 2.5300 0.75 1104 119 0.2719 0.3577
REMARK 3 10 2.5300 - 2.4428 0.74 1103 117 0.2756 0.3749
REMARK 3 11 2.4428 - 2.3666 0.71 1027 116 0.2620 0.3495
REMARK 3 12 2.3666 - 2.2990 0.70 1030 104 0.2585 0.3385
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) : 0.340
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.080
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.84
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 3391
REMARK 3 ANGLE : 1.152 4702
REMARK 3 CHIRALITY : 0.055 513
REMARK 3 PLANARITY : 0.007 494
REMARK 3 DIHEDRAL : 18.994 1935
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 6CRC 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_1000233073.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-MAY-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 : 19268
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300
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 (%) : 97.9
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.09400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34
REMARK 200 COMPLETENESS FOR SHELL (%) : 83.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : 0.47100
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 (%): 48.64
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39
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 39.46950
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: 5390 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20140 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 VAL A 303 CG1 CG2
REMARK 470 DG P 1 O6
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 OP2 DA T 14 O HOH T 101 1.94
REMARK 500 O HOH A 580 O HOH T 107 1.97
REMARK 500 N7 DG T 15 O HOH T 102 2.02
REMARK 500 OP1 DOC P 10 O HOH P 101 2.04
REMARK 500 O LYS A 60 O HOH A 501 2.07
REMARK 500 OE2 GLU A 295 O HOH A 502 2.10
REMARK 500 NZ LYS A 289 C ILE A 323 2.11
REMARK 500 OE1 GLU A 154 O HOH A 503 2.14
REMARK 500 O ALA A 307 O HOH A 504 2.14
REMARK 500 OP1 DT T 6 O HOH T 103 2.15
REMARK 500 O HOH A 524 O HOH A 585 2.16
REMARK 500 OG1 THR A 16 O HOH A 505 2.19
REMARK 500 O THR A 201 O HOH A 506 2.19
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 DC T 1 O3' DC T 1 C3' -0.043
REMARK 500 DC T 8 O3' DC T 8 C3' -0.051
REMARK 500 DC P 2 O3' DC P 2 C3' -0.056
REMARK 500 DG P 4 O3' DG P 4 C3' -0.040
REMARK 500 DG D 1 P DG D 1 OP3 -0.128
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 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DG T 15 O4' - C1' - N9 ANGL. DEV. = 2.3 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 -75.79 53.39
REMARK 500 ALA A 32 74.24 -111.38
REMARK 500 PRO A 50 30.91 -94.21
REMARK 500 ASP A 170 112.97 -163.39
REMARK 500 CYS A 178 -140.16 -105.26
REMARK 500 SER A 199 40.68 -88.46
REMARK 500 THR A 201 -52.58 -152.30
REMARK 500 SER A 202 -8.26 172.33
REMARK 500 GLU A 203 -92.91 -89.81
REMARK 500 PRO A 208 76.01 -52.34
REMARK 500 ASN A 245 -142.03 48.68
REMARK 500 ASP A 246 30.73 -96.70
REMARK 500 GLU A 295 -6.06 -53.87
REMARK 500 ALA A 307 -80.45 -175.31
REMARK 500 PRO A 312 76.24 -63.89
REMARK 500 LYS A 317 -120.65 -117.52
REMARK 500 ASP A 318 -50.51 64.02
REMARK 500 ILE A 319 -39.52 -39.71
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 -39.57
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 587 DISTANCE = 5.97 ANGSTROMS
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 61 O
REMARK 620 2 HOH A 501 O 88.6
REMARK 620 3 HOH D 103 O 150.8 96.5
REMARK 620 N 1 2
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 98.6
REMARK 620 3 ILE A 106 O 94.5 86.8
REMARK 620 4 DG P 9 OP1 155.7 97.8 104.3
REMARK 620 N 1 2 3
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 83.2
REMARK 620 3 VA7 A 401 O1A 64.0 64.7
REMARK 620 4 VA7 A 401 O1B 127.6 86.9 65.2
REMARK 620 5 VA7 A 401 O3G 118.9 150.3 105.3 64.1
REMARK 620 N 1 2 3 4
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 106.2
REMARK 620 3 ASP A 256 OD1 107.8 89.9
REMARK 620 4 VA7 A 401 O1A 76.5 83.1 172.7
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 VA7 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 6CRC A 1 335 UNP P06746 DPOLB_HUMAN 1 335
DBREF 6CRC T 1 16 PDB 6CRC 6CRC 1 16
DBREF 6CRC P 1 10 PDB 6CRC 6CRC 1 10
DBREF 6CRC D 1 5 PDB 6CRC 6CRC 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 DOC
SEQRES 1 D 5 DG DT DC DG DG
HET DOC P 10 18
HET VA7 A 401 32
HET MG A 402 1
HET NA A 403 1
HET NA A 404 1
HET NA A 405 1
HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
HETNAM VA7 2'-DEOXY-5'-O-[(R)-{[(R)-[DICHLORO(PHOSPHONO)
HETNAM 2 VA7 METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)
HETNAM 3 VA7 PHOSPHORYL]ADENOSINE
HETNAM MG MAGNESIUM ION
HETNAM NA SODIUM ION
FORMUL 3 DOC C9 H14 N3 O6 P
FORMUL 5 VA7 C11 H16 CL2 N5 O11 P3
FORMUL 6 MG MG 2+
FORMUL 7 NA 3(NA 1+)
FORMUL 10 HOH *118(H2 O)
HELIX 1 AA1 GLN A 8 LEU A 11 5 4
HELIX 2 AA2 ASN A 12 VAL A 29 1 18
HELIX 3 AA3 ALA A 32 TYR A 49 1 18
HELIX 4 AA4 SER A 55 LYS A 61 1 7
HELIX 5 AA5 GLY A 66 GLY A 80 1 15
HELIX 6 AA6 LEU A 82 GLN A 90 1 9
HELIX 7 AA7 ASP A 91 THR A 101 1 11
HELIX 8 AA8 GLY A 107 GLU A 117 1 11
HELIX 9 AA9 THR A 121 ASN A 128 1 8
HELIX 10 AB1 GLU A 129 LEU A 132 5 4
HELIX 11 AB2 ASN A 133 TYR A 142 1 10
HELIX 12 AB3 TYR A 142 GLU A 147 1 6
HELIX 13 AB4 ARG A 152 ASP A 170 1 19
HELIX 14 AB5 CYS A 178 ARG A 183 1 6
HELIX 15 AB6 LEU A 211 VAL A 221 1 11
HELIX 16 AB7 PRO A 261 ASP A 263 5 3
HELIX 17 AB8 GLN A 264 PHE A 272 1 9
HELIX 18 AB9 SER A 275 LYS A 289 1 15
HELIX 19 AC1 PHE A 320 GLN A 324 5 5
HELIX 20 AC2 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 HIS A 252 LEU A 259 1 O ARG A 258 N LEU A 195
SHEET 4 AA2 5 LYS A 234 GLN A 240 -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 NZ LYS A 289 O ILE A 323 1555 1555 1.27
LINK O3' DG P 9 P DOC P 10 1555 1555 1.61
LINK O LYS A 61 NA NA A 404 1555 1555 3.10
LINK O THR A 101 NA NA A 403 1555 1555 2.28
LINK O VAL A 103 NA NA A 403 1555 1555 2.58
LINK O ILE A 106 NA NA A 403 1555 1555 2.36
LINK OD1 ASP A 190 MG MG A 402 1555 1555 2.52
LINK OD2 ASP A 190 NA NA A 405 1555 1555 2.61
LINK OD2 ASP A 192 MG MG A 402 1555 1555 2.47
LINK OD1 ASP A 192 NA NA A 405 1555 1555 2.50
LINK OD1 ASP A 256 NA NA A 405 1555 1555 2.74
LINK O1A VA7 A 401 MG MG A 402 1555 1555 2.97
LINK O1B VA7 A 401 MG MG A 402 1555 1555 2.29
LINK O3G VA7 A 401 MG MG A 402 1555 1555 2.68
LINK O1A VA7 A 401 NA NA A 405 1555 1555 2.94
LINK NA NA A 403 OP1 DG P 9 1555 1555 2.35
LINK NA NA A 404 O HOH A 501 1555 1555 2.72
LINK NA NA A 404 O HOH D 103 1555 1555 2.50
CISPEP 1 GLY A 274 SER A 275 0 -0.67
SITE 1 AC1 21 ARG A 149 GLY A 179 SER A 180 ARG A 183
SITE 2 AC1 21 SER A 188 GLY A 189 ASP A 190 ASP A 192
SITE 3 AC1 21 TYR A 271 PHE A 272 GLY A 274 SER A 275
SITE 4 AC1 21 ASP A 276 ASN A 279 ARG A 283 MG A 402
SITE 5 AC1 21 NA A 405 HOH A 536 DOC P 10 DT T 6
SITE 6 AC1 21 DG T 7
SITE 1 AC2 3 ASP A 190 ASP A 192 VA7 A 401
SITE 1 AC3 4 THR A 101 VAL A 103 ILE A 106 DG P 9
SITE 1 AC4 4 LYS A 61 LEU A 62 HOH A 501 HOH D 103
SITE 1 AC5 5 ASP A 190 ASP A 192 ASP A 256 VA7 A 401
SITE 2 AC5 5 DOC P 10
CRYST1 54.437 78.939 54.911 90.00 108.55 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 0.018370 0.000000 0.006166 0.00000
SCALE2 0.000000 0.012668 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019210 0.00000