PDB Short entry for 5VZA HEADER TRANSFERASE/DNA 27-MAY-17 5VZA TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN POLYMERASE MU (G433S) 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 5VZA 1 LINK REVDAT 4 04-DEC-19 5VZA 1 REMARK REVDAT 3 27-SEP-17 5VZA 1 JRNL REVDAT 2 20-SEP-17 5VZA 1 REMARK REVDAT 1 05-JUL-17 5VZA 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 72169 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 3596 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 32.3797 - 4.4417 0.94 2731 142 0.1809 0.2215 REMARK 3 2 4.4417 - 3.5269 1.00 2761 144 0.1424 0.1411 REMARK 3 3 3.5269 - 3.0815 1.00 2748 146 0.1565 0.1692 REMARK 3 4 3.0815 - 2.7999 1.00 2704 143 0.1793 0.1927 REMARK 3 5 2.7999 - 2.5993 1.00 2692 140 0.1783 0.1783 REMARK 3 6 2.5993 - 2.4461 1.00 2723 143 0.1754 0.1901 REMARK 3 7 2.4461 - 2.3237 1.00 2675 142 0.1668 0.1665 REMARK 3 8 2.3237 - 2.2225 1.00 2678 139 0.1646 0.1885 REMARK 3 9 2.2225 - 2.1370 1.00 2681 141 0.1582 0.1790 REMARK 3 10 2.1370 - 2.0633 1.00 2669 142 0.1692 0.1808 REMARK 3 11 2.0633 - 1.9988 1.00 2672 140 0.1658 0.1869 REMARK 3 12 1.9988 - 1.9416 1.00 2671 141 0.1716 0.1686 REMARK 3 13 1.9416 - 1.8905 1.00 2683 143 0.1716 0.2062 REMARK 3 14 1.8905 - 1.8444 1.00 2670 140 0.1667 0.1901 REMARK 3 15 1.8444 - 1.8025 1.00 2647 140 0.1697 0.1899 REMARK 3 16 1.8025 - 1.7641 1.00 2629 138 0.1636 0.1932 REMARK 3 17 1.7641 - 1.7288 1.00 2679 141 0.1695 0.1675 REMARK 3 18 1.7288 - 1.6962 1.00 2669 140 0.1698 0.1919 REMARK 3 19 1.6962 - 1.6659 1.00 2624 139 0.1766 0.2007 REMARK 3 20 1.6659 - 1.6377 1.00 2695 142 0.1748 0.1930 REMARK 3 21 1.6377 - 1.6113 1.00 2638 139 0.1771 0.2043 REMARK 3 22 1.6113 - 1.5865 1.00 2657 139 0.1811 0.1943 REMARK 3 23 1.5865 - 1.5631 1.00 2630 139 0.1906 0.1922 REMARK 3 24 1.5631 - 1.5411 0.96 2555 134 0.1961 0.1904 REMARK 3 25 1.5411 - 1.5203 0.88 2312 119 0.2109 0.2501 REMARK 3 26 1.5203 - 1.5006 0.78 2080 100 0.2092 0.2189 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) : 16.630 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 : 0.006 3306 REMARK 3 ANGLE : 0.917 4603 REMARK 3 CHIRALITY : 0.056 505 REMARK 3 PLANARITY : 0.006 539 REMARK 3 DIHEDRAL : 12.530 1060 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): 12.9461 -18.4820 -14.6549 REMARK 3 T TENSOR REMARK 3 T11: 0.1195 T22: 0.1250 REMARK 3 T33: 0.1167 T12: 0.0472 REMARK 3 T13: -0.0023 T23: -0.0272 REMARK 3 L TENSOR REMARK 3 L11: 1.3862 L22: 1.3067 REMARK 3 L33: 1.6227 L12: -0.2207 REMARK 3 L13: 0.1226 L23: -0.4029 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.1744 S13: -0.1491 REMARK 3 S21: -0.1150 S22: -0.0883 S23: -0.1324 REMARK 3 S31: 0.1924 S32: 0.2565 S33: 0.0529 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 17.1320 8.1791 -17.0178 REMARK 3 T TENSOR REMARK 3 T11: 0.1553 T22: 0.1673 REMARK 3 T33: 0.2178 T12: -0.0116 REMARK 3 T13: 0.0610 T23: 0.0422 REMARK 3 L TENSOR REMARK 3 L11: 0.9555 L22: 0.9177 REMARK 3 L33: 2.1202 L12: -0.3515 REMARK 3 L13: -0.3396 L23: 0.7192 REMARK 3 S TENSOR REMARK 3 S11: 0.0923 S12: 0.1475 S13: 0.2049 REMARK 3 S21: -0.2805 S22: -0.0305 S23: -0.2963 REMARK 3 S31: -0.2579 S32: 0.1453 S33: -0.0032 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -1.9201 8.6398 -0.7108 REMARK 3 T TENSOR REMARK 3 T11: 0.0919 T22: 0.0788 REMARK 3 T33: 0.1031 T12: -0.0076 REMARK 3 T13: 0.0074 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 1.7602 L22: 1.6733 REMARK 3 L33: 0.4622 L12: -0.3725 REMARK 3 L13: -0.1562 L23: -0.0221 REMARK 3 S TENSOR REMARK 3 S11: 0.0605 S12: -0.1104 S13: 0.3299 REMARK 3 S21: 0.1144 S22: -0.0404 S23: -0.0669 REMARK 3 S31: -0.0954 S32: -0.0177 S33: -0.0149 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -10.9473 -10.1186 -11.2065 REMARK 3 T TENSOR REMARK 3 T11: 0.0708 T22: 0.0892 REMARK 3 T33: 0.0766 T12: -0.0023 REMARK 3 T13: -0.0145 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 1.4933 L22: 1.6633 REMARK 3 L33: 1.6275 L12: -0.1382 REMARK 3 L13: -0.3692 L23: 0.2686 REMARK 3 S TENSOR REMARK 3 S11: 0.0301 S12: 0.2455 S13: -0.1481 REMARK 3 S21: -0.1099 S22: -0.0603 S23: 0.1931 REMARK 3 S31: 0.0178 S32: -0.1982 S33: 0.0058 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 0.2771 -8.8634 -23.3875 REMARK 3 T TENSOR REMARK 3 T11: 0.1549 T22: 0.1844 REMARK 3 T33: 0.0574 T12: 0.0101 REMARK 3 T13: -0.0218 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 0.5881 L22: 0.9176 REMARK 3 L33: 0.5750 L12: 0.1219 REMARK 3 L13: 0.0174 L23: -0.0880 REMARK 3 S TENSOR REMARK 3 S11: 0.0652 S12: 0.2641 S13: -0.0711 REMARK 3 S21: -0.2182 S22: -0.0451 S23: 0.0348 REMARK 3 S31: 0.0389 S32: -0.0468 S33: -0.0254 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 5VZA 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_1000228181. 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 : 73268 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.56000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.940 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 (%): 51.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 90MM HEPES PH 7.5, 18% PEG4K, VAPOR REMARK 280 DIFFUSION, SITTING 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 29.93300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.02200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.41900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.02200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.93300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.41900 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: 4730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 CG CD OE1 OE2 REMARK 470 GLU A 218 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 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 OE1 NE2 REMARK 470 ASP A 356 CG OD1 OD2 REMARK 470 GLN A 357 OE1 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 145 O HOH A 801 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DT P 3 O3' DT P 3 C3' -0.057 REMARK 500 DG D 1 P DG D 1 OP3 -0.117 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 -159.95 -154.26 REMARK 500 ASN A 153 41.22 -140.45 REMARK 500 THR A 318 -152.00 -122.68 REMARK 500 THR A 318 -154.40 -129.13 REMARK 500 SER A 411 -144.17 -162.74 REMARK 500 ASN A 493 49.87 -88.26 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 A1137 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH T 145 DISTANCE = 5.99 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 96.5 REMARK 620 3 VAL A 246 O 89.1 92.9 REMARK 620 4 DT P 3 OP1 171.3 92.2 90.2 REMARK 620 5 HOH P 110 O 86.1 176.5 84.7 85.2 REMARK 620 6 HOH P 113 O 94.8 96.0 169.8 84.4 86.1 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 98.2 REMARK 620 3 ASP A 418 OD2 85.2 95.9 REMARK 620 4 2KH A 701 O2A 93.7 91.3 172.8 REMARK 620 5 HOH A 917 O 166.0 90.3 82.9 97.1 REMARK 620 6 DA P 4 O3' 165.9 90.4 82.9 97.2 0.1 REMARK 620 7 HOH P 105 O 87.2 172.5 89.7 83.2 85.5 85.3 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 94.4 REMARK 620 3 2KH A 701 O2A 94.0 90.0 REMARK 620 4 2KH A 701 O1B 172.6 92.5 88.5 REMARK 620 5 2KH A 701 O3G 86.7 178.8 90.2 86.3 REMARK 620 6 HOH A 937 O 86.8 88.5 178.4 90.9 91.2 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 EDO 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 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 5VZA A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 5VZA T 1 9 PDB 5VZA 5VZA 1 9 DBREF 5VZA P 1 4 PDB 5VZA 5VZA 1 4 DBREF 5VZA D 1 4 PDB 5VZA 5VZA 1 4 SEQADV 5VZA GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZA SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZA ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZA ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZA ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZA A UNP Q9NP87 PRO 398 DELETION SEQADV 5VZA A UNP Q9NP87 GLY 399 DELETION SEQADV 5VZA A UNP Q9NP87 ALA 400 DELETION SEQADV 5VZA A UNP Q9NP87 ALA 401 DELETION SEQADV 5VZA A UNP Q9NP87 VAL 402 DELETION SEQADV 5VZA A UNP Q9NP87 GLY 403 DELETION SEQADV 5VZA A UNP Q9NP87 GLY 404 DELETION SEQADV 5VZA A UNP Q9NP87 SER 405 DELETION SEQADV 5VZA A UNP Q9NP87 THR 406 DELETION SEQADV 5VZA A UNP Q9NP87 ARG 407 DELETION SEQADV 5VZA A UNP Q9NP87 PRO 408 DELETION SEQADV 5VZA A UNP Q9NP87 CYS 409 DELETION SEQADV 5VZA GLY A 410 UNP Q9NP87 PRO 410 LINKER SEQADV 5VZA SER 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 SER 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 EDO A 705 4 HET EDO A 706 4 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 EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 2KH C9 H16 N3 O14 P3 FORMUL 6 MG 2(MG 2+) FORMUL 8 NA NA 1+ FORMUL 9 EDO 2(C2 H6 O2) FORMUL 11 HOH *415(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 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 2.43 LINK O ILE A 243 NA NA A 704 1555 1555 2.39 LINK O VAL A 246 NA NA A 704 1555 1555 2.31 LINK OD2 ASP A 330 MG MG A 702 1555 1555 2.00 LINK OD1 ASP A 330 MG MG A 703 1555 1555 2.01 LINK OD1 ASP A 332 MG MG A 702 1555 1555 2.05 LINK OD2 ASP A 332 MG MG A 703 1555 1555 2.05 LINK OD2 ASP A 418 MG MG A 702 1555 1555 2.05 LINK O2A 2KH A 701 MG MG A 702 1555 1555 2.27 LINK O2A 2KH A 701 MG MG A 703 1555 1555 2.17 LINK O1B 2KH A 701 MG MG A 703 1555 1555 2.05 LINK O3G 2KH A 701 MG MG A 703 1555 1555 2.14 LINK MG MG A 702 O BHOH A 917 1555 1555 2.13 LINK MG MG A 702 O3'A DA P 4 1555 1555 2.14 LINK MG MG A 702 O HOH P 105 1555 1555 2.08 LINK MG MG A 703 O HOH A 937 1555 1555 2.11 LINK NA NA A 704 OP1 DT P 3 1555 1555 2.55 LINK NA NA A 704 O AHOH P 110 1555 1555 2.53 LINK NA NA A 704 O HOH P 113 1555 1555 2.39 CISPEP 1 GLY A 436 SER A 437 0 -4.13 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 SER A 433 TRP A 434 GLY A 436 LYS A 438 SITE 4 AC1 27 GLN A 441 MG A 702 MG A 703 HOH A 861 SITE 5 AC1 27 HOH A 868 HOH A 870 HOH A 917 HOH A 937 SITE 6 AC1 27 HOH A 951 HOH A 972 HOH A 981 HOH A1004 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 917 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 937 SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 DT P 3 SITE 2 AC4 6 HOH P 110 HOH P 113 SITE 1 AC5 5 PRO A 190 SER A 191 PRO A 192 GLN A 198 SITE 2 AC5 5 HOH A 848 SITE 1 AC6 4 PRO A 146 PRO A 488 GLN A 491 HOH A 885 CRYST1 59.866 68.838 110.044 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 0.016704 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009087 0.00000