HEADER TRANSFERASE 20-MAY-19 6P1N
TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 1-NT
TITLE 2 GAPPED SUBSTRATE CONTAINING TEMPLATE 8OG AND BOUND INCOMING DAMPNPP
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 6P1N 1 LINK
REVDAT 3 18-DEC-19 6P1N 1 REMARK
REVDAT 2 09-OCT-19 6P1N 1 JRNL
REVDAT 1 04-SEP-19 6P1N 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. 1.60 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) : 1.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.66
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 60585
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 : 0.187
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3027
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 26.6630 - 4.4766 1.00 2839 149 0.1668 0.1986
REMARK 3 2 4.4766 - 3.5559 1.00 2710 142 0.1405 0.1471
REMARK 3 3 3.5559 - 3.1072 1.00 2676 142 0.1565 0.1743
REMARK 3 4 3.1072 - 2.8234 1.00 2660 141 0.1808 0.1886
REMARK 3 5 2.8234 - 2.6212 1.00 2660 136 0.1806 0.2058
REMARK 3 6 2.6212 - 2.4668 1.00 2622 140 0.1780 0.1950
REMARK 3 7 2.4668 - 2.3433 1.00 2644 138 0.1659 0.1907
REMARK 3 8 2.3433 - 2.2414 1.00 2633 141 0.1668 0.1927
REMARK 3 9 2.2414 - 2.1551 1.00 2617 135 0.1642 0.1984
REMARK 3 10 2.1551 - 2.0808 1.00 2616 140 0.1640 0.1675
REMARK 3 11 2.0808 - 2.0158 1.00 2629 142 0.1643 0.1918
REMARK 3 12 2.0158 - 1.9582 1.00 2629 134 0.1693 0.2048
REMARK 3 13 1.9582 - 1.9066 1.00 2592 136 0.1719 0.1973
REMARK 3 14 1.9066 - 1.8601 1.00 2612 138 0.1643 0.2067
REMARK 3 15 1.8601 - 1.8179 1.00 2609 138 0.1690 0.2018
REMARK 3 16 1.8179 - 1.7792 1.00 2632 138 0.1736 0.2056
REMARK 3 17 1.7792 - 1.7436 1.00 2613 138 0.1802 0.1974
REMARK 3 18 1.7436 - 1.7107 1.00 2569 135 0.1745 0.2269
REMARK 3 19 1.7107 - 1.6801 1.00 2595 137 0.1704 0.1887
REMARK 3 20 1.6801 - 1.6517 1.00 2623 136 0.1706 0.2039
REMARK 3 21 1.6517 - 1.6250 0.99 2551 135 0.1851 0.1929
REMARK 3 22 1.6250 - 1.6000 0.86 2227 116 0.2056 0.2451
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) : 0.140
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.450
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 : 0.012 3184
REMARK 3 ANGLE : 1.238 4416
REMARK 3 CHIRALITY : 0.075 483
REMARK 3 PLANARITY : 0.009 517
REMARK 3 DIHEDRAL : 9.554 1675
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): 12.8393 -18.6530 -14.5790
REMARK 3 T TENSOR
REMARK 3 T11: 0.2128 T22: 0.2219
REMARK 3 T33: 0.2136 T12: 0.0340
REMARK 3 T13: 0.0014 T23: -0.0263
REMARK 3 L TENSOR
REMARK 3 L11: 0.7141 L22: 0.7161
REMARK 3 L33: 0.6652 L12: -0.2972
REMARK 3 L13: 0.3655 L23: -0.2624
REMARK 3 S TENSOR
REMARK 3 S11: 0.0330 S12: 0.1275 S13: -0.1295
REMARK 3 S21: -0.0278 S22: -0.0780 S23: -0.0892
REMARK 3 S31: 0.1258 S32: 0.1688 S33: -0.0000
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: ( CHAIN A AND RESID 232:289 )
REMARK 3 ORIGIN FOR THE GROUP (A): 17.0378 8.1993 -16.9609
REMARK 3 T TENSOR
REMARK 3 T11: 0.2374 T22: 0.2507
REMARK 3 T33: 0.3151 T12: -0.0001
REMARK 3 T13: 0.0654 T23: 0.0511
REMARK 3 L TENSOR
REMARK 3 L11: 0.2190 L22: 0.3066
REMARK 3 L33: 0.1966 L12: 0.0253
REMARK 3 L13: 0.0239 L23: 0.0714
REMARK 3 S TENSOR
REMARK 3 S11: 0.0790 S12: 0.0972 S13: 0.1847
REMARK 3 S21: -0.0897 S22: -0.0285 S23: -0.2360
REMARK 3 S31: -0.1687 S32: 0.0527 S33: 0.0000
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: ( CHAIN A AND RESID 290:423 )
REMARK 3 ORIGIN FOR THE GROUP (A): -2.1163 8.9875 -0.5940
REMARK 3 T TENSOR
REMARK 3 T11: 0.2022 T22: 0.1831
REMARK 3 T33: 0.2323 T12: -0.0025
REMARK 3 T13: 0.0154 T23: -0.0218
REMARK 3 L TENSOR
REMARK 3 L11: 0.8576 L22: 0.5254
REMARK 3 L33: 0.1627 L12: -0.0858
REMARK 3 L13: -0.0807 L23: -0.1617
REMARK 3 S TENSOR
REMARK 3 S11: 0.0991 S12: -0.0985 S13: 0.2600
REMARK 3 S21: 0.1181 S22: -0.0602 S23: -0.0551
REMARK 3 S31: -0.0424 S32: -0.0266 S33: 0.0005
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: ( CHAIN A AND RESID 424:494 )
REMARK 3 ORIGIN FOR THE GROUP (A): -11.0572 -10.3689 -11.3049
REMARK 3 T TENSOR
REMARK 3 T11: 0.1763 T22: 0.2044
REMARK 3 T33: 0.1862 T12: -0.0056
REMARK 3 T13: -0.0091 T23: -0.0108
REMARK 3 L TENSOR
REMARK 3 L11: 0.5246 L22: 0.7600
REMARK 3 L33: 0.8175 L12: -0.0813
REMARK 3 L13: -0.2819 L23: 0.2848
REMARK 3 S TENSOR
REMARK 3 S11: 0.0148 S12: 0.1586 S13: -0.0628
REMARK 3 S21: 0.0157 S22: -0.0515 S23: 0.1344
REMARK 3 S31: 0.0090 S32: -0.1314 S33: 0.0000
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): 0.2683 -7.1731 -23.1572
REMARK 3 T TENSOR
REMARK 3 T11: 0.2678 T22: 0.3128
REMARK 3 T33: 0.1814 T12: 0.0112
REMARK 3 T13: -0.0016 T23: -0.0158
REMARK 3 L TENSOR
REMARK 3 L11: 0.2102 L22: 0.3443
REMARK 3 L33: 0.2289 L12: 0.0129
REMARK 3 L13: 0.0925 L23: -0.2545
REMARK 3 S TENSOR
REMARK 3 S11: 0.0625 S12: 0.2400 S13: 0.0502
REMARK 3 S21: -0.1587 S22: -0.0163 S23: 0.0158
REMARK 3 S31: -0.0234 S32: -0.0854 S33: 0.0084
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 6P1N 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_1000241711.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-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 : 60668
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600
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 (%) : 99.6
REMARK 200 DATA REDUNDANCY : 3.100
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05700
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 96.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.10
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.33900
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: PHASER
REMARK 200 STARTING MODEL: 4M04
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 57.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86
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 29.96300
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.30450
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.38600
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.30450
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.96300
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.38600
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: 5790 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15900 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 GLN A 366
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 465 ASP A 383
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 GLN A 200 CD OE1 NE2
REMARK 470 GLU A 207 CD OE1 OE2
REMARK 470 GLU A 267 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 ASP A 296 OD1 OD2
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 OE1 NE2
REMARK 470 GLN A 357 OE1 NE2
REMARK 470 GLN A 364 CG CD OE1 NE2
REMARK 470 GLU A 465 CD OE1 OE2
REMARK 470 GLN A 466 CD OE1 NE2
REMARK 470 LYS A 467 CD CE NZ
REMARK 470 GLN A 471 OE1 NE2
REMARK 470 GLU A 485 OE1 OE2
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' -0.060
REMARK 500 DT P 3 O3' DT P 3 C3' -0.084
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 ARG A 322 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DA T 7 O5' - P - OP1 ANGL. DEV. = -6.6 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 ASN A 153 40.55 -140.44
REMARK 500 GLN A 268 61.77 -118.68
REMARK 500 THR A 318 -149.25 -123.16
REMARK 500 THR A 318 -155.79 -131.48
REMARK 500 SER A 411 -147.41 -164.63
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 T 138 DISTANCE = 6.52 ANGSTROMS
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 97.0
REMARK 620 3 VAL A 246 O 88.4 93.5
REMARK 620 4 DT P 3 OP1 171.8 91.2 90.2
REMARK 620 5 HOH P 111 O 87.7 175.3 86.6 84.2
REMARK 620 6 HOH P 114 O 92.9 96.6 169.5 87.0 83.0
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 100.8
REMARK 620 3 ASP A 418 OD2 86.8 96.3
REMARK 620 4 DZ4 A 501 O2A 93.9 89.8 173.6
REMARK 620 5 DA P 4 O3' 169.9 85.9 84.9 93.7
REMARK 620 6 HOH P 102 O 88.6 168.8 90.2 83.4 85.5
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 94.3
REMARK 620 3 DZ4 A 501 O2A 96.1 89.4
REMARK 620 4 DZ4 A 501 O2B 171.5 93.2 88.0
REMARK 620 5 DZ4 A 501 O2G 85.3 179.4 90.2 87.2
REMARK 620 6 HOH A 712 O 84.9 88.1 177.3 91.3 92.3
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 DZ4 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 CL 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
DBREF 6P1N A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494
DBREF 6P1N T 1 9 PDB 6P1N 6P1N 1 9
DBREF 6P1N P 1 4 PDB 6P1N 6P1N 1 4
DBREF 6P1N D 1 4 PDB 6P1N 6P1N 1 4
SEQADV 6P1N GLY A 129 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1N SER A 130 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1N ALA A 131 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1N ALA A 132 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1N ALA A 133 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1N A UNP Q9NP87 PRO 398 DELETION
SEQADV 6P1N A UNP Q9NP87 GLY 399 DELETION
SEQADV 6P1N A UNP Q9NP87 ALA 400 DELETION
SEQADV 6P1N A UNP Q9NP87 ALA 401 DELETION
SEQADV 6P1N A UNP Q9NP87 VAL 402 DELETION
SEQADV 6P1N A UNP Q9NP87 GLY 403 DELETION
SEQADV 6P1N A UNP Q9NP87 GLY 404 DELETION
SEQADV 6P1N A UNP Q9NP87 SER 405 DELETION
SEQADV 6P1N A UNP Q9NP87 THR 406 DELETION
SEQADV 6P1N A UNP Q9NP87 ARG 407 DELETION
SEQADV 6P1N A UNP Q9NP87 PRO 408 DELETION
SEQADV 6P1N A UNP Q9NP87 CYS 409 DELETION
SEQADV 6P1N 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 DZ4 A 501 30
HET MG A 502 1
HET MG A 503 1
HET NA A 504 1
HET CL A 505 1
HET CL A 506 1
HET EDO A 507 4
HET EPE A 508 6
HET EDO A 509 4
HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETNAM DZ4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 DZ4 PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE
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 DZ4 C10 H17 N6 O11 P3
FORMUL 6 MG 2(MG 2+)
FORMUL 8 NA NA 1+
FORMUL 9 CL 2(CL 1-)
FORMUL 11 EDO 2(C2 H6 O2)
FORMUL 12 EPE C8 H18 N2 O4 S
FORMUL 14 HOH *383(H2 O)
HELIX 1 AA1 TYR A 141 ARG A 145 5 5
HELIX 2 AA2 ASN A 153 GLU A 170 1 18
HELIX 3 AA3 SER A 172 LEU A 189 1 18
HELIX 4 AA4 THR A 195 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 LEU A 361 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 1.61
LINK O3' 8OG T 5 P DT T 6 1555 1555 1.60
LINK O THR A 241 NA NA A 504 1555 1555 2.43
LINK O ILE A 243 NA NA A 504 1555 1555 2.38
LINK O VAL A 246 NA NA A 504 1555 1555 2.33
LINK OD2 ASP A 330 MG MG A 502 1555 1555 1.99
LINK OD1 ASP A 330 MG MG A 503 1555 1555 2.00
LINK OD1 ASP A 332 MG MG A 502 1555 1555 2.06
LINK OD2 ASP A 332 MG MG A 503 1555 1555 1.96
LINK OD2 ASP A 418 MG MG A 502 1555 1555 2.04
LINK O2A DZ4 A 501 MG MG A 502 1555 1555 2.28
LINK O2A DZ4 A 501 MG MG A 503 1555 1555 2.14
LINK O2B DZ4 A 501 MG MG A 503 1555 1555 2.09
LINK O2G DZ4 A 501 MG MG A 503 1555 1555 2.16
LINK MG MG A 502 O3' DA P 4 1555 1555 2.20
LINK MG MG A 502 O HOH P 102 1555 1555 2.10
LINK MG MG A 503 O HOH A 712 1555 1555 2.11
LINK NA NA A 504 OP1 DT P 3 1555 1555 2.59
LINK NA NA A 504 O HOH P 111 1555 1555 2.36
LINK NA NA A 504 O HOH P 114 1555 1555 2.29
CISPEP 1 GLY A 436 SER A 437 0 -7.68
SITE 1 AC1 26 GLY A 319 GLY A 320 ARG A 323 LYS A 325
SITE 2 AC1 26 GLY A 328 HIS A 329 ASP A 330 ASP A 332
SITE 3 AC1 26 GLY A 433 TRP A 434 THR A 435 GLY A 436
SITE 4 AC1 26 LYS A 438 MG A 502 MG A 503 HOH A 658
SITE 5 AC1 26 HOH A 672 HOH A 685 HOH A 712 HOH A 734
SITE 6 AC1 26 HOH A 740 HOH A 762 HOH A 778 DA P 4
SITE 7 AC1 26 HOH P 102 8OG T 5
SITE 1 AC2 7 ASP A 330 ASP A 332 ASP A 418 DZ4 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 DZ4 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 DT P 3
SITE 2 AC4 6 HOH P 111 HOH P 114
SITE 1 AC5 2 SER A 458 DA T 7
SITE 1 AC6 4 SER A 172 GLY A 174 ARG A 175 EDO A 509
SITE 1 AC7 5 THR A 194 THR A 314 THR A 336 HOH A 647
SITE 2 AC7 5 HOH A 709
SITE 1 AC8 5 LYS A 325 LEU A 326 GLN A 327 HOH A 720
SITE 2 AC8 5 HOH A 727
SITE 1 AC9 4 GLY A 171 GLU A 173 GLY A 174 CL A 506
CRYST1 59.926 68.772 110.609 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 0.016687 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014541 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009041 0.00000