HEADER TRANSFERASE 20-MAY-19 6P1V
TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 1-NT
TITLE 2 GAPPED SUBSTRATE CONTAINING UNDAMAGED TEMPLATE DG AND BOUND INCOMING
TITLE 3 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*GP*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 6P1V 1 LINK
REVDAT 3 18-DEC-19 6P1V 1 REMARK
REVDAT 2 09-OCT-19 6P1V 1 JRNL
REVDAT 1 04-SEP-19 6P1V 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. 1.95 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) : 1.95
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.30
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 3 NUMBER OF REFLECTIONS : 33726
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.178
REMARK 3 R VALUE (WORKING SET) : 0.177
REMARK 3 FREE R VALUE : 0.204
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1686
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 31.3029 - 4.4595 1.00 2862 151 0.1680 0.2135
REMARK 3 2 4.4595 - 3.5412 1.00 2715 142 0.1482 0.1495
REMARK 3 3 3.5412 - 3.0940 1.00 2709 142 0.1685 0.1818
REMARK 3 4 3.0940 - 2.8113 1.00 2671 141 0.1978 0.2275
REMARK 3 5 2.8113 - 2.6099 1.00 2665 141 0.1961 0.2388
REMARK 3 6 2.6099 - 2.4561 1.00 2639 137 0.1911 0.2065
REMARK 3 7 2.4561 - 2.3331 1.00 2671 142 0.1838 0.2218
REMARK 3 8 2.3331 - 2.2316 1.00 2637 138 0.1813 0.2392
REMARK 3 9 2.2316 - 2.1457 1.00 2649 140 0.1827 0.2144
REMARK 3 10 2.1457 - 2.0717 1.00 2638 141 0.1857 0.2031
REMARK 3 11 2.0717 - 2.0069 1.00 2633 138 0.1985 0.2286
REMARK 3 12 2.0069 - 1.9496 0.96 2551 133 0.2204 0.2569
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) : 0.190
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.950
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 : 0.004 3130
REMARK 3 ANGLE : 0.627 4332
REMARK 3 CHIRALITY : 0.040 473
REMARK 3 PLANARITY : 0.003 506
REMARK 3 DIHEDRAL : 12.827 1010
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): 13.0369 -18.4393 -14.7915
REMARK 3 T TENSOR
REMARK 3 T11: 0.2136 T22: 0.2293
REMARK 3 T33: 0.2049 T12: 0.0317
REMARK 3 T13: 0.0014 T23: -0.0190
REMARK 3 L TENSOR
REMARK 3 L11: 0.2985 L22: 0.7940
REMARK 3 L33: 0.5118 L12: -0.2076
REMARK 3 L13: 0.2252 L23: -0.1523
REMARK 3 S TENSOR
REMARK 3 S11: 0.0346 S12: 0.1220 S13: -0.1289
REMARK 3 S21: -0.0202 S22: -0.0943 S23: -0.0439
REMARK 3 S31: 0.1462 S32: 0.1841 S33: 0.0000
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: ( CHAIN A AND RESID 232:289 )
REMARK 3 ORIGIN FOR THE GROUP (A): 17.2417 8.1703 -16.6791
REMARK 3 T TENSOR
REMARK 3 T11: 0.2414 T22: 0.2426
REMARK 3 T33: 0.2910 T12: -0.0069
REMARK 3 T13: 0.0438 T23: 0.0339
REMARK 3 L TENSOR
REMARK 3 L11: 0.2002 L22: 0.2562
REMARK 3 L33: 0.1598 L12: -0.1746
REMARK 3 L13: 0.0113 L23: 0.1227
REMARK 3 S TENSOR
REMARK 3 S11: 0.0871 S12: 0.0627 S13: 0.1650
REMARK 3 S21: -0.1261 S22: -0.0243 S23: -0.2075
REMARK 3 S31: -0.1506 S32: 0.0699 S33: -0.0000
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: ( CHAIN A AND RESID 290:423 )
REMARK 3 ORIGIN FOR THE GROUP (A): -1.8788 8.6187 -0.3655
REMARK 3 T TENSOR
REMARK 3 T11: 0.1689 T22: 0.1664
REMARK 3 T33: 0.1861 T12: 0.0041
REMARK 3 T13: 0.0023 T23: -0.0124
REMARK 3 L TENSOR
REMARK 3 L11: 0.4515 L22: 0.7852
REMARK 3 L33: 0.1997 L12: 0.0194
REMARK 3 L13: -0.3969 L23: 0.2469
REMARK 3 S TENSOR
REMARK 3 S11: 0.0613 S12: -0.1412 S13: 0.1252
REMARK 3 S21: 0.0970 S22: -0.0261 S23: -0.0381
REMARK 3 S31: -0.0266 S32: -0.0311 S33: 0.0002
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: ( CHAIN A AND RESID 424:494 )
REMARK 3 ORIGIN FOR THE GROUP (A): -11.2658 -10.1421 -11.4160
REMARK 3 T TENSOR
REMARK 3 T11: 0.1664 T22: 0.1891
REMARK 3 T33: 0.1814 T12: -0.0079
REMARK 3 T13: -0.0078 T23: -0.0169
REMARK 3 L TENSOR
REMARK 3 L11: 0.3426 L22: 0.4700
REMARK 3 L33: 0.3918 L12: 0.0121
REMARK 3 L13: -0.3513 L23: -0.0249
REMARK 3 S TENSOR
REMARK 3 S11: -0.0050 S12: 0.1494 S13: -0.0705
REMARK 3 S21: -0.0049 S22: -0.0137 S23: 0.1061
REMARK 3 S31: 0.0163 S32: -0.0968 S33: -0.0001
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): 0.2467 -7.0944 -23.0497
REMARK 3 T TENSOR
REMARK 3 T11: 0.2595 T22: 0.2767
REMARK 3 T33: 0.1693 T12: -0.0122
REMARK 3 T13: -0.0137 T23: -0.0137
REMARK 3 L TENSOR
REMARK 3 L11: 0.0201 L22: 0.2106
REMARK 3 L33: 0.1544 L12: 0.1039
REMARK 3 L13: 0.3487 L23: -0.0714
REMARK 3 S TENSOR
REMARK 3 S11: 0.0508 S12: 0.2157 S13: 0.0238
REMARK 3 S21: -0.2184 S22: -0.0076 S23: 0.0396
REMARK 3 S31: 0.0003 S32: -0.0666 S33: 0.1079
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 6P1V 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_1000241736.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-APR-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 : 33791
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950
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 (%) : 99.9
REMARK 200 DATA REDUNDANCY : 12.50
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.11500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8
REMARK 200 DATA REDUNDANCY IN SHELL : 7.90
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.60000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.730
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 (%): 56.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 80MM HEPES PH 7.5, 80MM NACL, 8% W/V
REMARK 280 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 29.95100
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.06250
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.30300
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.06250
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.95100
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.30300
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: 5450 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16050 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 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 365
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 LEU A 196 CD1 CD2
REMARK 470 GLN A 200 CD OE1 NE2
REMARK 470 GLU A 207 CD OE1 OE2
REMARK 470 GLU A 218 CD OE1 OE2
REMARK 470 GLU A 223 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 CD 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 LYS A 467 CD CE NZ
REMARK 470 GLN A 471 OE1 NE2
REMARK 470 GLU A 485 CD 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 DG D 1 P DG D 1 OP3 -0.126
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. = 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 ASN A 153 42.04 -143.31
REMARK 500 GLN A 268 70.03 -115.42
REMARK 500 THR A 318 -149.75 -126.54
REMARK 500 THR A 318 -152.57 -130.78
REMARK 500 SER A 411 -143.87 -167.76
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 137 DISTANCE = 6.58 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 98.4
REMARK 620 3 VAL A 246 O 93.7 94.0
REMARK 620 4 HOH A 829 O 85.0 84.9 178.2
REMARK 620 5 DT P 3 OP1 171.7 88.8 89.9 91.6
REMARK 620 6 HOH P 111 O 95.3 166.2 85.8 95.6 77.4
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 95.9
REMARK 620 3 ASP A 418 OD2 87.0 94.7
REMARK 620 4 0KX A 501 O2A 90.8 90.0 175.0
REMARK 620 5 DA P 4 O3' 172.5 85.9 85.5 96.5
REMARK 620 6 HOH P 102 O 89.6 172.1 91.2 84.2 89.4
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 90.6
REMARK 620 3 0KX A 501 O1G 84.3 174.9
REMARK 620 4 0KX A 501 O1B 170.7 97.6 87.5
REMARK 620 5 0KX A 501 O2A 97.8 90.7 89.6 86.5
REMARK 620 6 HOH A 710 O 82.9 88.6 91.2 92.9 179.0
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 CL A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 A 510
DBREF 6P1V A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494
DBREF 6P1V T 1 9 PDB 6P1V 6P1V 1 9
DBREF 6P1V P 1 4 PDB 6P1V 6P1V 1 4
DBREF 6P1V D 1 4 PDB 6P1V 6P1V 1 4
SEQADV 6P1V GLY A 129 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1V SER A 130 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1V ALA A 131 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1V ALA A 132 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1V ALA A 133 UNP Q9NP87 EXPRESSION TAG
SEQADV 6P1V A UNP Q9NP87 PRO 398 DELETION
SEQADV 6P1V A UNP Q9NP87 GLY 399 DELETION
SEQADV 6P1V A UNP Q9NP87 ALA 400 DELETION
SEQADV 6P1V A UNP Q9NP87 ALA 401 DELETION
SEQADV 6P1V A UNP Q9NP87 VAL 402 DELETION
SEQADV 6P1V A UNP Q9NP87 GLY 403 DELETION
SEQADV 6P1V A UNP Q9NP87 GLY 404 DELETION
SEQADV 6P1V A UNP Q9NP87 SER 405 DELETION
SEQADV 6P1V A UNP Q9NP87 THR 406 DELETION
SEQADV 6P1V A UNP Q9NP87 ARG 407 DELETION
SEQADV 6P1V A UNP Q9NP87 PRO 408 DELETION
SEQADV 6P1V A UNP Q9NP87 CYS 409 DELETION
SEQADV 6P1V 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 DG DT DA DC DG
SEQRES 1 P 4 DC DG DT DA
SEQRES 1 D 4 DG DC DC DG
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 CL A 506 1
HET CL A 507 1
HET EPE A 508 5
HET EDO A 509 4
HET EDO A 510 4
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 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EPE HEPES
HETSYN EDO ETHYLENE GLYCOL
FORMUL 5 0KX C9 H17 N4 O12 P3
FORMUL 6 MG 2(MG 2+)
FORMUL 8 NA NA 1+
FORMUL 9 CL 3(CL 1-)
FORMUL 12 EPE C8 H18 N2 O4 S
FORMUL 13 EDO 2(C2 H6 O2)
FORMUL 15 HOH *368(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 ARG A 230 1 9
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 GLN A 426 GLY A 436 1 11
HELIX 17 AB8 SER A 437 GLY A 453 1 17
HELIX 18 AB9 SER A 474 LEU A 482 1 9
HELIX 19 AC1 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 O THR A 241 NA NA A 504 1555 1555 2.33
LINK O ILE A 243 NA NA A 504 1555 1555 2.38
LINK O VAL A 246 NA NA A 504 1555 1555 2.31
LINK OD2 ASP A 330 MG MG A 502 1555 1555 2.04
LINK OD1 ASP A 330 MG MG A 503 1555 1555 2.03
LINK OD1 ASP A 332 MG MG A 502 1555 1555 2.05
LINK OD2 ASP A 332 MG MG A 503 1555 1555 2.09
LINK OD2 ASP A 418 MG MG A 502 1555 1555 2.05
LINK O2A 0KX A 501 MG MG A 502 1555 1555 2.37
LINK O1G 0KX A 501 MG MG A 503 1555 1555 2.08
LINK O1B 0KX A 501 MG MG A 503 1555 1555 1.98
LINK O2A 0KX A 501 MG MG A 503 1555 1555 2.10
LINK MG MG A 502 O3' DA P 4 1555 1555 2.22
LINK MG MG A 502 O HOH P 102 1555 1555 2.05
LINK MG MG A 503 O HOH A 710 1555 1555 2.21
LINK NA NA A 504 O HOH A 829 1555 1555 2.43
LINK NA NA A 504 OP1 DT P 3 1555 1555 2.88
LINK NA NA A 504 O HOH P 111 1555 1555 2.28
CISPEP 1 GLY A 436 SER A 437 0 -2.92
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 509 HOH A 659
SITE 5 AC1 27 HOH A 676 HOH A 710 HOH A 712 HOH A 724
SITE 6 AC1 27 HOH A 752 HOH A 772 HOH A 773 HOH A 786
SITE 7 AC1 27 DA P 4 HOH P 102 DG 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 710
SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 HOH A 829
SITE 2 AC4 6 DT P 3 HOH P 111
SITE 1 AC5 5 ARG A 387 ARG A 445 SER A 458 EDO A 509
SITE 2 AC5 5 DA T 7
SITE 1 AC6 2 THR A 468 PHE A 469
SITE 1 AC7 3 SER A 172 GLY A 174 ARG A 175
SITE 1 AC8 4 LYS A 325 LEU A 326 GLN A 327 HOH A 653
SITE 1 AC9 8 ARG A 387 GLY A 433 TRP A 434 ARG A 445
SITE 2 AC9 8 SER A 458 0KX A 501 CL A 505 DA P 4
SITE 1 AD1 3 PRO A 190 SER A 191 GLN A 198
CRYST1 59.902 68.606 110.125 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 0.016694 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014576 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009081 0.00000