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 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 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