HEADER TRANSFERASE/DNA 27-MAY-17 5VZ7
TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN POLYMERASE MU (G433A) MUTANT
TITLE 2 WITH INCOMING NONHYDROLYZABLE UMPNPP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 134-494;
COMPND 5 SYNONYM: POL MU,TERMINAL TRANSFERASE;
COMPND 6 EC: 2.7.7.7;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3');
COMPND 11 CHAIN: T;
COMPND 12 ENGINEERED: YES;
COMPND 13 MOL_ID: 3;
COMPND 14 MOLECULE: DNA (5'-D(*CP*GP*TP*A)-3');
COMPND 15 CHAIN: P;
COMPND 16 ENGINEERED: YES;
COMPND 17 MOL_ID: 4;
COMPND 18 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3');
COMPND 19 CHAIN: D;
COMPND 20 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_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEXM;
SOURCE 10 MOL_ID: 2;
SOURCE 11 SYNTHETIC: YES;
SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 13 ORGANISM_TAXID: 32630;
SOURCE 14 MOL_ID: 3;
SOURCE 15 SYNTHETIC: YES;
SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 17 ORGANISM_TAXID: 32630;
SOURCE 18 MOL_ID: 4;
SOURCE 19 SYNTHETIC: YES;
SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 21 ORGANISM_TAXID: 32630
KEYWDS FAMILY X, NONHOMOLOGOUS END-JOINING, DNA DOUBLE STRAND BREAK REPAIR,
KEYWDS 2 RIBONUCLEOTIDE INCORPORATION, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.F.MOON,J.M.PRYOR,D.A.RAMSDEN,T.A.KUNKEL,K.BEBENEK,L.C.PEDERSEN
REVDAT 5 04-OCT-23 5VZ7 1 LINK
REVDAT 4 04-DEC-19 5VZ7 1 REMARK
REVDAT 3 27-SEP-17 5VZ7 1 JRNL
REVDAT 2 20-SEP-17 5VZ7 1 REMARK
REVDAT 1 05-JUL-17 5VZ7 0
JRNL AUTH A.F.MOON,J.M.PRYOR,D.A.RAMSDEN,T.A.KUNKEL,K.BEBENEK,
JRNL AUTH 2 L.C.PEDERSEN
JRNL TITL STRUCTURAL ACCOMMODATION OF RIBONUCLEOTIDE INCORPORATION BY
JRNL TITL 2 THE DNA REPAIR ENZYME POLYMERASE MU.
JRNL REF NUCLEIC ACIDS RES. V. 45 9138 2017
JRNL REFN ESSN 1362-4962
JRNL PMID 28911097
JRNL DOI 10.1093/NAR/GKX527
REMARK 2
REMARK 2 RESOLUTION. 1.55 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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.44
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0
REMARK 3 NUMBER OF REFLECTIONS : 63709
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.171
REMARK 3 R VALUE (WORKING SET) : 0.170
REMARK 3 FREE R VALUE : 0.188
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990
REMARK 3 FREE R VALUE TEST SET COUNT : 3180
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 40.4484 - 4.4087 0.97 2868 154 0.1776 0.2221
REMARK 3 2 4.4087 - 3.4999 1.00 2792 147 0.1384 0.1379
REMARK 3 3 3.4999 - 3.0577 1.00 2808 148 0.1600 0.1788
REMARK 3 4 3.0577 - 2.7782 1.00 2772 145 0.1815 0.2058
REMARK 3 5 2.7782 - 2.5791 1.00 2769 145 0.1818 0.1858
REMARK 3 6 2.5791 - 2.4270 1.00 2749 147 0.1747 0.1771
REMARK 3 7 2.4270 - 2.3055 1.00 2722 138 0.1631 0.1845
REMARK 3 8 2.3055 - 2.2052 1.00 2738 151 0.1677 0.1900
REMARK 3 9 2.2052 - 2.1203 1.00 2735 145 0.1628 0.1769
REMARK 3 10 2.1203 - 2.0471 1.00 2733 141 0.1680 0.1910
REMARK 3 11 2.0471 - 1.9831 1.00 2695 145 0.1669 0.1769
REMARK 3 12 1.9831 - 1.9264 1.00 2743 142 0.1726 0.2016
REMARK 3 13 1.9264 - 1.8757 1.00 2707 142 0.1736 0.1800
REMARK 3 14 1.8757 - 1.8299 1.00 2729 143 0.1753 0.2055
REMARK 3 15 1.8299 - 1.7883 1.00 2714 144 0.1738 0.1979
REMARK 3 16 1.7883 - 1.7503 1.00 2721 143 0.1746 0.1758
REMARK 3 17 1.7503 - 1.7153 1.00 2684 141 0.1789 0.2087
REMARK 3 18 1.7153 - 1.6829 1.00 2725 143 0.1862 0.1988
REMARK 3 19 1.6829 - 1.6528 0.99 2692 140 0.1916 0.2159
REMARK 3 20 1.6528 - 1.6248 0.96 2587 136 0.1939 0.1938
REMARK 3 21 1.6248 - 1.5986 0.87 2354 125 0.2033 0.2496
REMARK 3 22 1.5986 - 1.5740 0.77 2067 111 0.2038 0.2249
REMARK 3 23 1.5740 - 1.5509 0.52 1425 64 0.2154 0.2144
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
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) : 0.120
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.180
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 3275
REMARK 3 ANGLE : 1.057 4561
REMARK 3 CHIRALITY : 0.059 503
REMARK 3 PLANARITY : 0.007 532
REMARK 3 DIHEDRAL : 12.552 1046
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 137:231
REMARK 3 ORIGIN FOR THE GROUP (A): 12.8626 -18.5987 -14.6161
REMARK 3 T TENSOR
REMARK 3 T11: 0.1163 T22: 0.1176
REMARK 3 T33: 0.1141 T12: 0.0427
REMARK 3 T13: 0.0000 T23: -0.0302
REMARK 3 L TENSOR
REMARK 3 L11: 1.2405 L22: 1.1631
REMARK 3 L33: 1.4823 L12: -0.2286
REMARK 3 L13: 0.2373 L23: -0.3582
REMARK 3 S TENSOR
REMARK 3 S11: 0.0213 S12: 0.1574 S13: -0.1511
REMARK 3 S21: -0.1061 S22: -0.0799 S23: -0.1319
REMARK 3 S31: 0.1507 S32: 0.2477 S33: 0.0567
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN A AND RESID 232:289
REMARK 3 ORIGIN FOR THE GROUP (A): 17.1801 7.9784 -16.7285
REMARK 3 T TENSOR
REMARK 3 T11: 0.1451 T22: 0.1659
REMARK 3 T33: 0.2122 T12: -0.0160
REMARK 3 T13: 0.0591 T23: 0.0405
REMARK 3 L TENSOR
REMARK 3 L11: 0.9608 L22: 1.1742
REMARK 3 L33: 1.7500 L12: -0.4045
REMARK 3 L13: -0.3552 L23: 0.7881
REMARK 3 S TENSOR
REMARK 3 S11: 0.0939 S12: 0.1442 S13: 0.1945
REMARK 3 S21: -0.2958 S22: -0.0182 S23: -0.3216
REMARK 3 S31: -0.2565 S32: 0.1448 S33: -0.0384
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN A AND RESID 290:423
REMARK 3 ORIGIN FOR THE GROUP (A): -2.0595 8.7709 -0.7118
REMARK 3 T TENSOR
REMARK 3 T11: 0.0755 T22: 0.0762
REMARK 3 T33: 0.1064 T12: -0.0074
REMARK 3 T13: 0.0060 T23: -0.0229
REMARK 3 L TENSOR
REMARK 3 L11: 1.6205 L22: 1.4855
REMARK 3 L33: 0.5195 L12: -0.2664
REMARK 3 L13: -0.0564 L23: 0.0282
REMARK 3 S TENSOR
REMARK 3 S11: 0.0463 S12: -0.1206 S13: 0.3229
REMARK 3 S21: 0.1253 S22: -0.0310 S23: -0.0438
REMARK 3 S31: -0.1026 S32: -0.0335 S33: -0.0063
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN A AND RESID 424:494
REMARK 3 ORIGIN FOR THE GROUP (A): -11.3440 -10.3251 -11.4058
REMARK 3 T TENSOR
REMARK 3 T11: 0.0593 T22: 0.0895
REMARK 3 T33: 0.0815 T12: -0.0095
REMARK 3 T13: -0.0167 T23: -0.0191
REMARK 3 L TENSOR
REMARK 3 L11: 1.4437 L22: 1.5544
REMARK 3 L33: 1.5244 L12: -0.2088
REMARK 3 L13: -0.3436 L23: 0.2346
REMARK 3 S TENSOR
REMARK 3 S11: 0.0269 S12: 0.2196 S13: -0.1804
REMARK 3 S21: -0.1039 S22: -0.0548 S23: 0.2335
REMARK 3 S31: 0.0794 S32: -0.2208 S33: -0.0168
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D
REMARK 3 ORIGIN FOR THE GROUP (A): 0.2415 -8.8969 -23.3463
REMARK 3 T TENSOR
REMARK 3 T11: 0.1486 T22: 0.1767
REMARK 3 T33: 0.0457 T12: 0.0181
REMARK 3 T13: -0.0258 T23: -0.0220
REMARK 3 L TENSOR
REMARK 3 L11: 0.7826 L22: 0.8391
REMARK 3 L33: 0.3986 L12: 0.1212
REMARK 3 L13: -0.0206 L23: -0.0139
REMARK 3 S TENSOR
REMARK 3 S11: 0.1332 S12: 0.3576 S13: -0.1321
REMARK 3 S21: -0.2934 S22: -0.1612 S23: 0.1106
REMARK 3 S31: 0.0228 S32: -0.1088 S33: -0.0258
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 5VZ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-17.
REMARK 100 THE DEPOSITION ID IS D_1000228172.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-APR-17
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK MONOCHROMATOR
REMARK 200 HIGH-RESOLUTION DOUBLE-CRYSTAL
REMARK 200 SI(220) SAGITTAL FOCUSING
REMARK 200 OPTICS : ROSENBAUM-ROCK VERTICAL FOCUSING
REMARK 200 MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66226
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550
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 (%) : 99.8
REMARK 200 DATA REDUNDANCY : 6.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3
REMARK 200 DATA REDUNDANCY IN SHELL : 4.10
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.67500
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.130
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 (%): 51.01
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM HEPES PH 7.5, 10% PEG4K, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K
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 29.90250
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.87850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.41250
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.87850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.90250
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.41250
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: 4740 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 16330 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 170 CD OE1 OE2
REMARK 470 GLN A 200 CD OE1 NE2
REMARK 470 GLU A 207 CD OE1 OE2
REMARK 470 ARG A 211 NE CZ NH1 NH2
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 284 CD OE1 NE2
REMARK 470 SER A 293 OG
REMARK 470 ASP A 296 CG OD1 OD2
REMARK 470 GLN A 300 CD OE1 NE2
REMARK 470 GLU A 304 CD OE1 OE2
REMARK 470 LYS A 339 CD CE NZ
REMARK 470 GLN A 355 CD OE1 NE2
REMARK 470 ASP A 356 CG OD1 OD2
REMARK 470 GLN A 357 OE1 NE2
REMARK 470 HIS A 363 ND1 CD2 CE1 NE2
REMARK 470 GLN A 364 CG CD OE1 NE2
REMARK 470 GLU A 465 CG CD OE1 OE2
REMARK 470 LYS A 467 CD CE NZ
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 DT P 3 O3' DT P 3 C3' -0.059
REMARK 500 DG D 1 P DG D 1 OP3 -0.122
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 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.5 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 THR A 318 -150.03 -124.03
REMARK 500 THR A 318 -157.39 -129.44
REMARK 500 PRO A 397 109.76 -53.67
REMARK 500 SER A 411 -144.08 -164.42
REMARK 500 ASN A 493 49.96 -87.81
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 707
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 704 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 241 O
REMARK 620 2 ILE A 243 O 96.0
REMARK 620 3 VAL A 246 O 88.4 92.5
REMARK 620 4 DT P 3 OP1 171.8 92.2 90.5
REMARK 620 5 HOH P 111 O 85.6 174.2 81.9 86.2
REMARK 620 6 HOH P 114 O 93.5 97.8 169.2 86.0 87.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 702 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 85.4 94.7
REMARK 620 4 2KH A 701 O2A 93.7 91.8 173.5
REMARK 620 5 HOH A 942 O 166.1 87.1 82.6 97.4
REMARK 620 6 DA P 4 O3' 166.1 87.2 82.6 97.4 0.1
REMARK 620 7 HOH P 105 O 88.7 170.1 88.8 84.8 84.2 84.1
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 703 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 330 OD1
REMARK 620 2 ASP A 332 OD2 93.9
REMARK 620 3 2KH A 701 O2A 94.7 90.0
REMARK 620 4 2KH A 701 O1B 173.1 92.4 87.8
REMARK 620 5 2KH A 701 O3G 86.2 178.0 92.0 87.4
REMARK 620 6 HOH A 902 O 85.7 87.6 177.6 92.1 90.4
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 2KH A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 703
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 704
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 705
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 706
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 707
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5TWP RELATED DB: PDB
REMARK 900 RELATED ID: 5TWQ RELATED DB: PDB
REMARK 900 RELATED ID: 5TWR RELATED DB: PDB
REMARK 900 RELATED ID: 5TWS RELATED DB: PDB
DBREF 5VZ7 A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494
DBREF 5VZ7 T 1 9 PDB 5VZ7 5VZ7 1 9
DBREF 5VZ7 P 1 4 PDB 5VZ7 5VZ7 1 4
DBREF 5VZ7 D 1 4 PDB 5VZ7 5VZ7 1 4
SEQADV 5VZ7 GLY A 129 UNP Q9NP87 EXPRESSION TAG
SEQADV 5VZ7 SER A 130 UNP Q9NP87 EXPRESSION TAG
SEQADV 5VZ7 ALA A 131 UNP Q9NP87 EXPRESSION TAG
SEQADV 5VZ7 ALA A 132 UNP Q9NP87 EXPRESSION TAG
SEQADV 5VZ7 ALA A 133 UNP Q9NP87 EXPRESSION TAG
SEQADV 5VZ7 A UNP Q9NP87 PRO 398 DELETION
SEQADV 5VZ7 A UNP Q9NP87 GLY 399 DELETION
SEQADV 5VZ7 A UNP Q9NP87 ALA 400 DELETION
SEQADV 5VZ7 A UNP Q9NP87 ALA 401 DELETION
SEQADV 5VZ7 A UNP Q9NP87 VAL 402 DELETION
SEQADV 5VZ7 A UNP Q9NP87 GLY 403 DELETION
SEQADV 5VZ7 A UNP Q9NP87 GLY 404 DELETION
SEQADV 5VZ7 A UNP Q9NP87 SER 405 DELETION
SEQADV 5VZ7 A UNP Q9NP87 THR 406 DELETION
SEQADV 5VZ7 A UNP Q9NP87 ARG 407 DELETION
SEQADV 5VZ7 A UNP Q9NP87 PRO 408 DELETION
SEQADV 5VZ7 A UNP Q9NP87 CYS 409 DELETION
SEQADV 5VZ7 GLY A 410 UNP Q9NP87 PRO 410 LINKER
SEQADV 5VZ7 ALA A 433 UNP Q9NP87 GLY 433 ENGINEERED MUTATION
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 ALA 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 DA DT DA DC DG
SEQRES 1 P 4 DC DG DT DA
SEQRES 1 D 4 DG DC DC DG
HET 2KH A 701 29
HET MG A 702 1
HET MG A 703 1
HET NA A 704 1
HET CL A 705 1
HET EDO A 706 4
HET EPE A 707 10
HETNAM 2KH 5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 2KH PHOSPHORYL]AMINO}PHOSPHORYL]URIDINE
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 EDO ETHYLENE GLYCOL
HETSYN EPE HEPES
FORMUL 5 2KH C9 H16 N3 O14 P3
FORMUL 6 MG 2(MG 2+)
FORMUL 8 NA NA 1+
FORMUL 9 CL CL 1-
FORMUL 10 EDO C2 H6 O2
FORMUL 11 EPE C8 H18 N2 O4 S
FORMUL 12 HOH *397(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 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 GLU A 267 1 7
HELIX 10 AB1 GLN A 268 LEU A 272 5 5
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 O THR A 241 NA NA A 704 1555 1555 2.41
LINK O ILE A 243 NA NA A 704 1555 1555 2.41
LINK O VAL A 246 NA NA A 704 1555 1555 2.33
LINK OD2 ASP A 330 MG MG A 702 1555 1555 1.97
LINK OD1 ASP A 330 MG MG A 703 1555 1555 2.01
LINK OD1 ASP A 332 MG MG A 702 1555 1555 2.04
LINK OD2 ASP A 332 MG MG A 703 1555 1555 2.06
LINK OD2 ASP A 418 MG MG A 702 1555 1555 2.10
LINK O2A 2KH A 701 MG MG A 702 1555 1555 2.28
LINK O2A 2KH A 701 MG MG A 703 1555 1555 2.16
LINK O1B 2KH A 701 MG MG A 703 1555 1555 2.05
LINK O3G 2KH A 701 MG MG A 703 1555 1555 2.09
LINK MG MG A 702 O BHOH A 942 1555 1555 2.16
LINK MG MG A 702 O3'A DA P 4 1555 1555 2.17
LINK MG MG A 702 O HOH P 105 1555 1555 2.06
LINK MG MG A 703 O HOH A 902 1555 1555 2.15
LINK NA NA A 704 OP1 DT P 3 1555 1555 2.53
LINK NA NA A 704 O AHOH P 111 1555 1555 2.55
LINK NA NA A 704 O HOH P 114 1555 1555 2.36
CISPEP 1 GLY A 436 SER A 437 0 -5.51
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 ALA A 433 TRP A 434 GLY A 436 LYS A 438
SITE 4 AC1 27 MG A 702 MG A 703 CL A 705 HOH A 837
SITE 5 AC1 27 HOH A 873 HOH A 874 HOH A 888 HOH A 902
SITE 6 AC1 27 HOH A 907 HOH A 937 HOH A 942 HOH A 954
SITE 7 AC1 27 DA P 4 HOH P 105 DA T 5
SITE 1 AC2 8 ASP A 330 ASP A 332 ASP A 418 2KH A 701
SITE 2 AC2 8 MG A 703 HOH A 942 DA P 4 HOH P 105
SITE 1 AC3 5 ASP A 330 ASP A 332 2KH A 701 MG A 702
SITE 2 AC3 5 HOH A 902
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 3 TRP A 434 ARG A 445 2KH A 701
SITE 1 AC6 4 PRO A 190 SER A 191 PRO A 192 GLN A 198
SITE 1 AC7 5 LYS A 325 LEU A 326 GLN A 327 HOH A 827
SITE 2 AC7 5 HOH A 838
CRYST1 59.805 68.825 109.757 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 0.016721 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014530 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009111 0.00000