PDB Short entry for 5VZD HEADER TRANSFERASE/DNA 27-MAY-17 5VZD TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN POLYMERASE MU (W434A) 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: UNP 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 DNA POLYMERASE, NONHOMOLOGOUS END-JOINING, DNA DOUBLE STRAND KEYWDS 2 BREAK REPAIR, 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 3 04-DEC-19 5VZD 1 REMARK REVDAT 2 27-SEP-17 5VZD 1 JRNL REVDAT 1 05-JUL-17 5VZD 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. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 59767 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2992 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 32.3357 - 4.4175 0.95 2804 148 0.1751 0.2136 REMARK 3 2 4.4175 - 3.5077 1.00 2769 147 0.1439 0.1357 REMARK 3 3 3.5077 - 3.0647 1.00 2797 145 0.1599 0.1682 REMARK 3 4 3.0647 - 2.7846 1.00 2751 147 0.1791 0.2036 REMARK 3 5 2.7846 - 2.5851 1.00 2739 143 0.1767 0.1881 REMARK 3 6 2.5851 - 2.4328 1.00 2743 145 0.1701 0.1776 REMARK 3 7 2.4328 - 2.3110 1.00 2701 140 0.1630 0.1819 REMARK 3 8 2.3110 - 2.2104 1.00 2733 146 0.1581 0.1882 REMARK 3 9 2.2104 - 2.1253 1.00 2708 143 0.1608 0.1659 REMARK 3 10 2.1253 - 2.0520 1.00 2716 142 0.1660 0.1852 REMARK 3 11 2.0520 - 1.9878 1.00 2714 149 0.1635 0.1853 REMARK 3 12 1.9878 - 1.9310 1.00 2685 133 0.1643 0.1890 REMARK 3 13 1.9310 - 1.8802 1.00 2722 147 0.1680 0.1649 REMARK 3 14 1.8802 - 1.8343 1.00 2703 142 0.1622 0.1875 REMARK 3 15 1.8343 - 1.7926 1.00 2702 142 0.1626 0.2017 REMARK 3 16 1.7926 - 1.7545 1.00 2681 141 0.1646 0.1799 REMARK 3 17 1.7545 - 1.7194 1.00 2676 141 0.1709 0.2063 REMARK 3 18 1.7194 - 1.6869 1.00 2690 142 0.1769 0.1967 REMARK 3 19 1.6869 - 1.6568 1.00 2704 141 0.1809 0.2387 REMARK 3 20 1.6568 - 1.6287 0.97 2614 137 0.1870 0.1966 REMARK 3 21 1.6287 - 1.6025 0.91 2423 131 0.2023 0.2105 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.330 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 3285 REMARK 3 ANGLE : 1.090 4564 REMARK 3 CHIRALITY : 0.060 499 REMARK 3 PLANARITY : 0.008 535 REMARK 3 DIHEDRAL : 9.819 1710 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESID 138:231 REMARK 3 ORIGIN FOR THE GROUP (A): 12.9531 -18.5905 -14.6759 REMARK 3 T TENSOR REMARK 3 T11: 0.1202 T22: 0.1360 REMARK 3 T33: 0.1026 T12: 0.0491 REMARK 3 T13: -0.0046 T23: -0.0299 REMARK 3 L TENSOR REMARK 3 L11: 1.4325 L22: 1.4910 REMARK 3 L33: 1.4182 L12: -0.2756 REMARK 3 L13: -0.0587 L23: -0.2828 REMARK 3 S TENSOR REMARK 3 S11: 0.0478 S12: 0.2182 S13: -0.1615 REMARK 3 S21: -0.1522 S22: -0.0944 S23: -0.1357 REMARK 3 S31: 0.1839 S32: 0.2592 S33: 0.0597 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 17.1506 7.9443 -17.0443 REMARK 3 T TENSOR REMARK 3 T11: 0.1629 T22: 0.2014 REMARK 3 T33: 0.2728 T12: -0.0043 REMARK 3 T13: 0.0977 T23: 0.0696 REMARK 3 L TENSOR REMARK 3 L11: 1.1344 L22: 0.8179 REMARK 3 L33: 2.0057 L12: 0.0806 REMARK 3 L13: -0.8448 L23: 0.5857 REMARK 3 S TENSOR REMARK 3 S11: 0.1221 S12: 0.2169 S13: 0.3439 REMARK 3 S21: -0.3247 S22: 0.0011 S23: -0.3889 REMARK 3 S31: -0.2935 S32: 0.2065 S33: -0.0713 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -1.8137 8.7457 -0.9693 REMARK 3 T TENSOR REMARK 3 T11: 0.0873 T22: 0.0859 REMARK 3 T33: 0.1607 T12: -0.0065 REMARK 3 T13: 0.0178 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 1.6226 L22: 1.4023 REMARK 3 L33: 0.4736 L12: 0.1969 REMARK 3 L13: -0.1736 L23: 0.1988 REMARK 3 S TENSOR REMARK 3 S11: 0.0837 S12: -0.1685 S13: 0.4517 REMARK 3 S21: 0.1132 S22: -0.0600 S23: -0.1006 REMARK 3 S31: -0.1167 S32: -0.0426 S33: -0.0155 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -11.3653 -10.4397 -11.4196 REMARK 3 T TENSOR REMARK 3 T11: 0.0709 T22: 0.1066 REMARK 3 T33: 0.0861 T12: -0.0011 REMARK 3 T13: -0.0184 T23: -0.0220 REMARK 3 L TENSOR REMARK 3 L11: 1.1134 L22: 1.6048 REMARK 3 L33: 1.5266 L12: 0.1930 REMARK 3 L13: -0.1462 L23: 0.1918 REMARK 3 S TENSOR REMARK 3 S11: 0.0282 S12: 0.2331 S13: -0.1643 REMARK 3 S21: -0.1038 S22: -0.0539 S23: 0.2329 REMARK 3 S31: 0.0497 S32: -0.2303 S33: -0.0019 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 0.2452 -9.0151 -23.3592 REMARK 3 T TENSOR REMARK 3 T11: 0.1661 T22: 0.2248 REMARK 3 T33: 0.0691 T12: 0.0112 REMARK 3 T13: -0.0247 T23: -0.0273 REMARK 3 L TENSOR REMARK 3 L11: 0.5564 L22: 0.9267 REMARK 3 L33: 0.9331 L12: -0.0227 REMARK 3 L13: -0.1170 L23: 0.3113 REMARK 3 S TENSOR REMARK 3 S11: 0.0734 S12: 0.3849 S13: -0.0227 REMARK 3 S21: -0.2571 S22: -0.0379 S23: 0.0357 REMARK 3 S31: 0.0472 S32: -0.0876 S33: 0.0076 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 5VZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228187. 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 : 60138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.65000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.360 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: 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 29.90900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.92750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.42050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.92750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.90900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.42050 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: 5080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 CG CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 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 OE1 NE2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 GLN A 364 OE1 NE2 REMARK 470 GLU A 465 CG 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: 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 OE2 GLU A 158 O HOH A 801 2.11 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 DC T 1 O3' DC T 1 C3' -0.040 REMARK 500 DT T 6 O3' DT T 6 C3' -0.043 REMARK 500 DT P 3 O3' DT P 3 C3' -0.044 REMARK 500 DG D 1 P DG D 1 OP3 -0.121 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA T 7 O4' - C1' - N9 ANGL. DEV. = 2.9 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 39.72 -140.56 REMARK 500 THR A 318 -155.81 -125.52 REMARK 500 SER A 411 -143.43 -163.17 REMARK 500 ASN A 493 48.20 -87.15 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 98.0 REMARK 620 3 VAL A 246 O 88.7 93.2 REMARK 620 4 DT P 3 OP1 169.9 92.1 90.6 REMARK 620 5 HOH P 111 O 85.2 175.8 84.2 84.6 REMARK 620 6 HOH P 112 O 92.6 94.1 172.3 86.8 88.4 REMARK 620 N 1 2 3 4 5 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 93.0 REMARK 620 3 2KH A 701 O2A 94.5 89.3 REMARK 620 4 2KH A 701 O1B 173.8 91.6 89.7 REMARK 620 5 2KH A 701 O3G 87.2 178.9 91.7 88.1 REMARK 620 6 HOH A 899 O 85.0 87.3 176.6 91.1 91.7 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 100.2 REMARK 620 3 ASP A 418 OD2 82.8 96.6 REMARK 620 4 DA P 4 O3' 164.7 87.9 83.4 REMARK 620 5 2KH A 701 O2A 96.2 91.8 171.6 96.5 REMARK 620 6 HOH A 848 O 167.4 83.2 84.8 4.8 95.8 REMARK 620 7 HOH A 855 O 86.1 171.7 89.6 87.3 82.0 91.9 REMARK 620 N 1 2 3 4 5 6 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 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 5VZD A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 5VZD T 1 9 PDB 5VZD 5VZD 1 9 DBREF 5VZD P 1 4 PDB 5VZD 5VZD 1 4 DBREF 5VZD D 1 4 PDB 5VZD 5VZD 1 4 SEQADV 5VZD GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZD SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZD ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZD ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZD ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZD A UNP Q9NP87 PRO 398 DELETION SEQADV 5VZD A UNP Q9NP87 GLY 399 DELETION SEQADV 5VZD A UNP Q9NP87 ALA 400 DELETION SEQADV 5VZD A UNP Q9NP87 ALA 401 DELETION SEQADV 5VZD A UNP Q9NP87 VAL 402 DELETION SEQADV 5VZD A UNP Q9NP87 GLY 403 DELETION SEQADV 5VZD A UNP Q9NP87 GLY 404 DELETION SEQADV 5VZD A UNP Q9NP87 SER 405 DELETION SEQADV 5VZD A UNP Q9NP87 THR 406 DELETION SEQADV 5VZD A UNP Q9NP87 ARG 407 DELETION SEQADV 5VZD A UNP Q9NP87 PRO 408 DELETION SEQADV 5VZD A UNP Q9NP87 CYS 409 DELETION SEQADV 5VZD GLY A 410 UNP Q9NP87 PRO 410 LINKER SEQADV 5VZD ALA A 434 UNP Q9NP87 TRP 434 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 GLY ALA 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 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 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 EDO 2(C2 H6 O2) FORMUL 11 EPE C8 H18 N2 O4 S FORMUL 12 HOH *378(H2 O) HELIX 1 AA1 TYR A 141 ARG A 145 5 5 HELIX 2 AA2 ASN A 153 GLU A 170 1 18 HELIX 3 AA3 SER A 172 LEU A 189 1 18 HELIX 4 AA4 THR A 195 GLN A 200 5 6 HELIX 5 AA5 GLY A 206 GLY A 220 1 15 HELIX 6 AA6 CYS A 222 SER A 231 1 10 HELIX 7 AA7 SER A 231 GLN A 242 1 12 HELIX 8 AA8 GLY A 247 GLU A 257 1 11 HELIX 9 AA9 THR A 261 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 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 704 1555 1555 2.44 LINK O ILE A 243 NA NA A 704 1555 1555 2.38 LINK O VAL A 246 NA NA A 704 1555 1555 2.30 LINK OD1 ASP A 330 MG MG A 703 1555 1555 2.00 LINK OD2 ASP A 330 MG MG A 702 1555 1555 1.99 LINK OD1 ASP A 332 MG MG A 702 1555 1555 2.04 LINK OD2 ASP A 332 MG MG A 703 1555 1555 2.05 LINK OD2 ASP A 418 MG MG A 702 1555 1555 2.10 LINK OP1 DT P 3 NA NA A 704 1555 1555 2.60 LINK O3'A DA P 4 MG MG A 702 1555 1555 2.18 LINK O2A 2KH A 701 MG MG A 702 1555 1555 2.19 LINK O2A 2KH A 701 MG MG A 703 1555 1555 2.18 LINK O1B 2KH A 701 MG MG A 703 1555 1555 2.05 LINK O3G 2KH A 701 MG MG A 703 1555 1555 2.11 LINK MG MG A 702 O BHOH A 848 1555 1555 1.97 LINK MG MG A 702 O HOH A 855 1555 1555 2.10 LINK MG MG A 703 O HOH A 899 1555 1555 2.12 LINK NA NA A 704 O HOH P 111 1555 1555 2.54 LINK NA NA A 704 O HOH P 112 1555 1555 2.38 CISPEP 1 GLY A 436 SER A 437 0 -4.88 SITE 1 AC1 28 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC1 28 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC1 28 GLY A 433 ALA A 434 THR A 435 GLY A 436 SITE 4 AC1 28 LYS A 438 MG A 702 MG A 703 HOH A 806 SITE 5 AC1 28 HOH A 809 HOH A 848 HOH A 854 HOH A 855 SITE 6 AC1 28 HOH A 877 HOH A 886 HOH A 899 HOH A 909 SITE 7 AC1 28 HOH A 931 HOH A 975 DA P 4 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 848 HOH A 855 DA P 4 SITE 1 AC3 5 ASP A 330 ASP A 332 2KH A 701 MG A 702 SITE 2 AC3 5 HOH A 899 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 112 SITE 1 AC5 5 ARG A 387 ALA A 434 HOH A 809 HOH A 827 SITE 2 AC5 5 DA P 4 SITE 1 AC6 5 PRO A 190 SER A 191 GLN A 198 HOH A 833 SITE 2 AC6 5 HOH A 930 SITE 1 AC7 5 LYS A 325 LEU A 326 GLN A 327 HOH A 828 SITE 2 AC7 5 HOH A 838 CRYST1 59.818 68.841 109.855 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 0.016717 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009103 0.00000