HEADER TRANSFERASE 20-MAY-19 6P1P
TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 1-NT
TITLE 2 GAPPED SUBSTRATE CONTAINING TEMPLATE 8OG AND BOUND INCOMING DCMPNPP
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;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3');
COMPND 9 CHAIN: T;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: DNA (5'-D(*CP*GP*TP*A)-3');
COMPND 13 CHAIN: P;
COMPND 14 ENGINEERED: YES;
COMPND 15 MOL_ID: 4;
COMPND 16 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3');
COMPND 17 CHAIN: D;
COMPND 18 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: POLM, POLMU;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 (DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEXM;
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 FAMILY X POLYMERASE, NHEJ, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.M.KAMINSKI,L.C.PEDERSEN,K.BEBENEK,K.K.CHIRUVELLA,D.A.RAMSDEN,
AUTHOR 2 T.A.KUNKEL
REVDAT 4 11-OCT-23 6P1P 1 LINK
REVDAT 3 18-DEC-19 6P1P 1 REMARK
REVDAT 2 09-OCT-19 6P1P 1 JRNL
REVDAT 1 04-SEP-19 6P1P 0
JRNL AUTH A.M.KAMINSKI,K.K.CHIRUVELLA,D.A.RAMSDEN,T.A.KUNKEL,
JRNL AUTH 2 K.BEBENEK,L.C.PEDERSEN
JRNL TITL UNEXPECTED BEHAVIOR OF DNA POLYMERASE MU OPPOSITE TEMPLATE
JRNL TITL 2 8-OXO-7,8-DIHYDRO-2'-GUANOSINE.
JRNL REF NUCLEIC ACIDS RES. V. 47 9410 2019
JRNL REFN ESSN 1362-4962
JRNL PMID 31435651
JRNL DOI 10.1093/NAR/GKZ680
REMARK 2
REMARK 2 RESOLUTION. 1.75 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) : 1.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.08
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 46304
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.166
REMARK 3 R VALUE (WORKING SET) : 0.165
REMARK 3 FREE R VALUE : 0.184
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990
REMARK 3 FREE R VALUE TEST SET COUNT : 2310
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 25.0827 - 4.4829 1.00 2807 147 0.1574 0.2020
REMARK 3 2 4.4829 - 3.5615 1.00 2676 142 0.1364 0.1458
REMARK 3 3 3.5615 - 3.1122 1.00 2658 138 0.1592 0.1631
REMARK 3 4 3.1122 - 2.8281 1.00 2627 143 0.1819 0.1890
REMARK 3 5 2.8281 - 2.6256 1.00 2616 134 0.1841 0.2018
REMARK 3 6 2.6256 - 2.4710 1.00 2613 136 0.1776 0.2003
REMARK 3 7 2.4710 - 2.3473 1.00 2607 139 0.1644 0.1781
REMARK 3 8 2.3473 - 2.2452 1.00 2617 139 0.1673 0.2064
REMARK 3 9 2.2452 - 2.1588 1.00 2581 134 0.1635 0.1629
REMARK 3 10 2.1588 - 2.0844 1.00 2605 138 0.1681 0.1735
REMARK 3 11 2.0844 - 2.0192 1.00 2571 136 0.1684 0.1970
REMARK 3 12 2.0192 - 1.9615 1.00 2596 138 0.1678 0.2105
REMARK 3 13 1.9615 - 1.9099 1.00 2594 134 0.1707 0.2136
REMARK 3 14 1.9099 - 1.8633 1.00 2573 136 0.1722 0.1808
REMARK 3 15 1.8633 - 1.8210 1.00 2577 137 0.1839 0.2036
REMARK 3 16 1.8210 - 1.7822 0.95 2470 128 0.2006 0.2092
REMARK 3 17 1.7822 - 1.7466 0.86 2206 111 0.2336 0.2629
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) : 0.170
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.440
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 3198
REMARK 3 ANGLE : 1.086 4433
REMARK 3 CHIRALITY : 0.059 483
REMARK 3 PLANARITY : 0.007 521
REMARK 3 DIHEDRAL : 9.789 1677
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 5
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ( CHAIN A AND RESID 138:231 )
REMARK 3 ORIGIN FOR THE GROUP (A): 12.6227 -18.6391 -14.5320
REMARK 3 T TENSOR
REMARK 3 T11: 0.2060 T22: 0.2031
REMARK 3 T33: 0.2084 T12: 0.0273
REMARK 3 T13: 0.0013 T23: -0.0262
REMARK 3 L TENSOR
REMARK 3 L11: 1.0023 L22: 1.0990
REMARK 3 L33: 1.2128 L12: -0.2999
REMARK 3 L13: -0.0173 L23: -0.3589
REMARK 3 S TENSOR
REMARK 3 S11: 0.0049 S12: 0.1100 S13: -0.1709
REMARK 3 S21: -0.0669 S22: -0.0786 S23: -0.1030
REMARK 3 S31: 0.1634 S32: 0.1918 S33: 0.0694
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: ( CHAIN A AND RESID 232:289 )
REMARK 3 ORIGIN FOR THE GROUP (A): 17.0833 8.0750 -16.7087
REMARK 3 T TENSOR
REMARK 3 T11: 0.2413 T22: 0.2345
REMARK 3 T33: 0.2963 T12: -0.0162
REMARK 3 T13: 0.0476 T23: 0.0288
REMARK 3 L TENSOR
REMARK 3 L11: 1.0004 L22: 0.7558
REMARK 3 L33: 1.3389 L12: -0.3765
REMARK 3 L13: -0.4517 L23: 0.8718
REMARK 3 S TENSOR
REMARK 3 S11: 0.0910 S12: 0.0846 S13: 0.1805
REMARK 3 S21: -0.2276 S22: -0.0003 S23: -0.2701
REMARK 3 S31: -0.2139 S32: 0.1313 S33: -0.0675
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: ( CHAIN A AND RESID 290:423 )
REMARK 3 ORIGIN FOR THE GROUP (A): -1.8632 9.0071 -0.4977
REMARK 3 T TENSOR
REMARK 3 T11: 0.1920 T22: 0.1832
REMARK 3 T33: 0.1921 T12: -0.0004
REMARK 3 T13: 0.0016 T23: -0.0137
REMARK 3 L TENSOR
REMARK 3 L11: 1.5986 L22: 1.1983
REMARK 3 L33: 0.3651 L12: -0.0240
REMARK 3 L13: -0.2873 L23: 0.2764
REMARK 3 S TENSOR
REMARK 3 S11: 0.0425 S12: -0.0900 S13: 0.2550
REMARK 3 S21: 0.1124 S22: -0.0282 S23: -0.0482
REMARK 3 S31: -0.0968 S32: -0.0009 S33: -0.0053
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: ( CHAIN A AND RESID 424:494 )
REMARK 3 ORIGIN FOR THE GROUP (A): -10.9216 -10.2628 -11.0675
REMARK 3 T TENSOR
REMARK 3 T11: 0.1839 T22: 0.2010
REMARK 3 T33: 0.1913 T12: -0.0089
REMARK 3 T13: -0.0111 T23: -0.0142
REMARK 3 L TENSOR
REMARK 3 L11: 1.1911 L22: 1.1676
REMARK 3 L33: 1.1944 L12: 0.1717
REMARK 3 L13: -0.1901 L23: 0.3745
REMARK 3 S TENSOR
REMARK 3 S11: -0.0024 S12: 0.2077 S13: -0.1061
REMARK 3 S21: -0.0899 S22: -0.0421 S23: 0.1981
REMARK 3 S31: 0.0455 S32: -0.1812 S33: 0.0394
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: ( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID 1:9
REMARK 3 ) OR ( CHAIN D AND RESID 1:4 )
REMARK 3 ORIGIN FOR THE GROUP (A): 0.2535 -7.0616 -23.0726
REMARK 3 T TENSOR
REMARK 3 T11: 0.2414 T22: 0.2792
REMARK 3 T33: 0.1810 T12: 0.0012
REMARK 3 T13: -0.0129 T23: -0.0116
REMARK 3 L TENSOR
REMARK 3 L11: 0.3576 L22: 0.9278
REMARK 3 L33: 0.7833 L12: -0.2097
REMARK 3 L13: 0.0371 L23: 0.0905
REMARK 3 S TENSOR
REMARK 3 S11: 0.0712 S12: 0.2650 S13: -0.0552
REMARK 3 S21: -0.2022 S22: -0.0787 S23: 0.0585
REMARK 3 S31: 0.0749 S32: -0.0798 S33: -0.0004
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 6P1P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-19.
REMARK 100 THE DEPOSITION ID IS D_1000241714.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-MAR-15
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 : MIRRORS
REMARK 200 OPTICS : VARIMAX HF
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000
REMARK 200 DATA SCALING SOFTWARE : HKL-3000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46401
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 12.80
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05100
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 49.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78
REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.25400
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.340
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: 4M04
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.80
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.5, 100MM NACL, 10%
REMARK 280 W.V PEG4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-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 29.97000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.14100
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.30400
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.14100
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.97000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.30400
REMARK 290 SMTRY3 4 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: 6040 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15980 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 GLY A 129
REMARK 465 SER A 130
REMARK 465 ALA A 131
REMARK 465 ALA A 132
REMARK 465 ALA A 133
REMARK 465 SER A 134
REMARK 465 PRO A 135
REMARK 465 ALA A 136
REMARK 465 TRP A 137
REMARK 465 HIS A 367
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 GLU A 173 CG CD OE1 OE2
REMARK 470 ARG A 175 CZ NH1 NH2
REMARK 470 GLN A 200 CD OE1 NE2
REMARK 470 GLU A 207 CD OE1 OE2
REMARK 470 GLU A 218 CG CD OE1 OE2
REMARK 470 GLU A 223 CD OE1 OE2
REMARK 470 GLU A 267 CG CD OE1 OE2
REMARK 470 GLN A 268 CG CD OE1 NE2
REMARK 470 GLN A 270 CG CD OE1 NE2
REMARK 470 LYS A 271 CG CD CE NZ
REMARK 470 GLN A 274 CG CD OE1 NE2
REMARK 470 GLN A 300 CD OE1 NE2
REMARK 470 GLU A 304 OE1 OE2
REMARK 470 LYS A 339 CD CE NZ
REMARK 470 GLN A 355 CD OE1 NE2
REMARK 470 GLN A 357 OE1 NE2
REMARK 470 GLN A 364 CG CD OE1 NE2
REMARK 470 ASP A 383 CG OD1 OD2
REMARK 470 GLU A 465 CD OE1 OE2
REMARK 470 GLN A 466 CG CD OE1 NE2
REMARK 470 LYS A 467 CD CE NZ
REMARK 470 GLN A 471 OE1 NE2
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 DG D 1 P DG D 1 OP3 -0.118
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 DT T 6 O4' - C1' - N1 ANGL. DEV. = 3.8 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 HIS A 151 -159.34 -151.24
REMARK 500 ASN A 153 40.35 -141.68
REMARK 500 LEU A 310 94.08 -160.10
REMARK 500 THR A 318 -149.29 -125.28
REMARK 500 THR A 318 -152.66 -130.20
REMARK 500 SER A 411 -144.50 -164.77
REMARK 500 ASN A 493 49.93 -88.23
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 EPE A 508
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 504 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 241 O
REMARK 620 2 ILE A 243 O 97.6
REMARK 620 3 VAL A 246 O 92.1 93.7
REMARK 620 4 HOH A 838 O 84.3 84.6 175.7
REMARK 620 5 DT P 3 OP1 173.1 88.8 90.1 93.7
REMARK 620 6 HOH P 110 O 93.6 167.8 90.6 91.9 79.8
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 502 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 330 OD2
REMARK 620 2 ASP A 332 OD1 100.0
REMARK 620 3 ASP A 418 OD2 87.7 94.0
REMARK 620 4 0KX A 501 O2A 94.6 91.8 173.3
REMARK 620 5 DA P 4 O3' 168.3 86.3 82.0 95.0
REMARK 620 6 HOH P 102 O 89.7 169.5 90.4 83.3 84.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 503 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 330 OD1
REMARK 620 2 ASP A 332 OD2 93.4
REMARK 620 3 0KX A 501 O1G 84.9 178.2
REMARK 620 4 0KX A 501 O1B 170.2 94.6 87.2
REMARK 620 5 0KX A 501 O2A 95.8 89.7 89.8 89.9
REMARK 620 6 HOH A 712 O 84.1 88.7 91.8 90.4 178.4
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 0KX A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 508
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO T 101
DBREF 6P1P A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494
DBREF 6P1P T 1 9 PDB 6P1P 6P1P 1 9
DBREF 6P1P P 1 4 PDB 6P1P 6P1P 1 4
DBREF 6P1P D 1 4 PDB 6P1P 6P1P 1 4
SEQADV 6P1P GLY A 129 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1P SER A 130 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1P ALA A 131 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1P ALA A 132 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1P ALA A 133 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1P A UNP Q9NP87 PRO 398 DELETION
SEQADV 6P1P A UNP Q9NP87 GLY 399 DELETION
SEQADV 6P1P A UNP Q9NP87 ALA 400 DELETION
SEQADV 6P1P A UNP Q9NP87 ALA 401 DELETION
SEQADV 6P1P A UNP Q9NP87 VAL 402 DELETION
SEQADV 6P1P A UNP Q9NP87 GLY 403 DELETION
SEQADV 6P1P A UNP Q9NP87 GLY 404 DELETION
SEQADV 6P1P A UNP Q9NP87 SER 405 DELETION
SEQADV 6P1P A UNP Q9NP87 THR 406 DELETION
SEQADV 6P1P A UNP Q9NP87 ARG 407 DELETION
SEQADV 6P1P A UNP Q9NP87 PRO 408 DELETION
SEQADV 6P1P A UNP Q9NP87 CYS 409 DELETION
SEQADV 6P1P GLY A 410 UNP Q9NP87 PRO 410 LINKER
SEQRES 1 A 354 GLY SER ALA ALA ALA SER PRO ALA TRP MET PRO ALA TYR
SEQRES 2 A 354 ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS ASN THR
SEQRES 3 A 354 GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU ALA ALA
SEQRES 4 A 354 GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR PHE CYS
SEQRES 5 A 354 ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER PRO VAL
SEQRES 6 A 354 THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS PHE GLY
SEQRES 7 A 354 GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU GLU HIS
SEQRES 8 A 354 GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG SER GLU
SEQRES 9 A 354 ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE PHE GLY
SEQRES 10 A 354 VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG GLU GLY
SEQRES 11 A 354 LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO GLN LYS
SEQRES 12 A 354 LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS HIS GLN
SEQRES 13 A 354 ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL ASP ALA
SEQRES 14 A 354 LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN ALA LEU
SEQRES 15 A 354 PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE ARG ARG
SEQRES 16 A 354 GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU ILE THR
SEQRES 17 A 354 HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU PRO ARG
SEQRES 18 A 354 VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE LEU TYR
SEQRES 19 A 354 HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO THR ARG
SEQRES 20 A 354 LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU ARG SER
SEQRES 21 A 354 PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER TRP LYS
SEQRES 22 A 354 ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL SER GLN
SEQRES 23 A 354 PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER LYS LEU
SEQRES 24 A 354 PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS GLU LYS
SEQRES 25 A 354 GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP PRO GLU
SEQRES 26 A 354 GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU ASP ILE
SEQRES 27 A 354 PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO GLU GLN
SEQRES 28 A 354 ARG ASN ALA
SEQRES 1 T 9 DC DG DG DC 8OG DT DA DC DG
SEQRES 1 P 4 DC DG DT DA
SEQRES 1 D 4 DG DC DC DG
HET 8OG T 5 23
HET 0KX A 501 28
HET MG A 502 1
HET MG A 503 1
HET NA A 504 1
HET CL A 505 1
HET EDO A 506 4
HET EDO A 507 4
HET EPE A 508 5
HET EDO A 509 4
HET EDO T 101 4
HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
HETNAM MG MAGNESIUM ION
HETNAM NA SODIUM ION
HETNAM CL CHLORIDE ION
HETNAM EDO 1,2-ETHANEDIOL
HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETSYN EDO ETHYLENE GLYCOL
HETSYN EPE HEPES
FORMUL 2 8OG C10 H14 N5 O8 P
FORMUL 5 0KX C9 H17 N4 O12 P3
FORMUL 6 MG 2(MG 2+)
FORMUL 8 NA NA 1+
FORMUL 9 CL CL 1-
FORMUL 10 EDO 4(C2 H6 O2)
FORMUL 12 EPE C8 H18 N2 O4 S
FORMUL 15 HOH *369(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 ALA A 188 1 17
HELIX 4 AA4 THR A 195 GLN A 200 5 6
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 GLN A 242 1 12
HELIX 8 AA8 GLY A 247 GLU A 257 1 11
HELIX 9 AA9 THR A 261 GLN A 268 1 8
HELIX 10 AB1 PRO A 269 LEU A 272 5 4
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 LEU A 334 N THR A 316
SHEET 3 AA2 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335
SHEET 4 AA2 5 ARG A 387 GLN A 396 -1 N PHE A 392 O VAL A 415
SHEET 5 AA2 5 ILE A 360 TYR A 362 -1 N TYR A 362 O ILE A 391
SHEET 1 AA3 3 TRP A 455 ASN A 457 0
SHEET 2 AA3 3 GLY A 460 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 O3' DC T 4 P 8OG T 5 1555 1555 1.60
LINK O3' 8OG T 5 P DT T 6 1555 1555 1.60
LINK O THR A 241 NA NA A 504 1555 1555 2.36
LINK O ILE A 243 NA NA A 504 1555 1555 2.40
LINK O VAL A 246 NA NA A 504 1555 1555 2.26
LINK OD2 ASP A 330 MG MG A 502 1555 1555 2.00
LINK OD1 ASP A 330 MG MG A 503 1555 1555 2.04
LINK OD1 ASP A 332 MG MG A 502 1555 1555 2.03
LINK OD2 ASP A 332 MG MG A 503 1555 1555 2.06
LINK OD2 ASP A 418 MG MG A 502 1555 1555 2.11
LINK O2A 0KX A 501 MG MG A 502 1555 1555 2.21
LINK O1G 0KX A 501 MG MG A 503 1555 1555 2.11
LINK O1B 0KX A 501 MG MG A 503 1555 1555 2.04
LINK O2A 0KX A 501 MG MG A 503 1555 1555 2.14
LINK MG MG A 502 O3' DA P 4 1555 1555 2.23
LINK MG MG A 502 O HOH P 102 1555 1555 2.08
LINK MG MG A 503 O HOH A 712 1555 1555 2.15
LINK NA NA A 504 O HOH A 838 1555 1555 2.44
LINK NA NA A 504 OP1 DT P 3 1555 1555 2.86
LINK NA NA A 504 O HOH P 110 1555 1555 2.34
CISPEP 1 GLY A 436 SER A 437 0 -6.71
SITE 1 AC1 27 GLY A 319 GLY A 320 ARG A 323 LYS A 325
SITE 2 AC1 27 GLY A 328 HIS A 329 ASP A 330 ASP A 332
SITE 3 AC1 27 GLY A 433 TRP A 434 GLY A 436 LYS A 438
SITE 4 AC1 27 MG A 502 MG A 503 EDO A 506 HOH A 640
SITE 5 AC1 27 HOH A 712 HOH A 715 HOH A 720 HOH A 730
SITE 6 AC1 27 HOH A 745 HOH A 753 HOH A 772 HOH A 788
SITE 7 AC1 27 DA P 4 HOH P 102 8OG T 5
SITE 1 AC2 7 ASP A 330 ASP A 332 ASP A 418 0KX A 501
SITE 2 AC2 7 MG A 503 DA P 4 HOH P 102
SITE 1 AC3 5 ASP A 330 ASP A 332 0KX A 501 MG A 502
SITE 2 AC3 5 HOH A 712
SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 HOH A 838
SITE 2 AC4 6 DT P 3 HOH P 110
SITE 1 AC5 3 ARG A 445 SER A 458 DA T 7
SITE 1 AC6 7 ARG A 387 GLY A 433 TRP A 434 ARG A 445
SITE 2 AC6 7 SER A 458 0KX A 501 DA P 4
SITE 1 AC7 4 CYS A 180 LYS A 438 ARG A 442 HOH A 750
SITE 1 AC8 5 LEU A 149 LYS A 325 LEU A 326 GLN A 327
SITE 2 AC8 5 HOH A 731
SITE 1 AC9 5 THR A 154 GLY A 155 GLU A 476 HOH A 782
SITE 2 AC9 5 HOH A 884
SITE 1 AD1 4 DC T 4 8OG T 5 HOH T 201 HOH T 202
CRYST1 59.940 68.608 110.282 90.00 90.00 90.00 P 21 21 21 4
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 0.016683 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014576 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009068 0.00000