PDB Short entry for 5VZG HEADER TRANSFERASE/DNA 27-MAY-17 5VZG TITLE PRE-CATALYTIC TERNARY COMPLEX OF HUMAN POLYMERASE MU (W434H) 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 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*GP*TP*A)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 18 CHAIN: D; COMPND 19 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 4 04-OCT-23 5VZG 1 LINK REVDAT 3 04-DEC-19 5VZG 1 SEQADV REVDAT 2 27-SEP-17 5VZG 1 JRNL REVDAT 1 05-JUL-17 5VZG 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. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 38510 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1937 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 34.8516 - 4.4534 1.00 2853 151 0.1783 0.2192 REMARK 3 2 4.4534 - 3.5359 1.00 2721 143 0.1450 0.1508 REMARK 3 3 3.5359 - 3.0892 1.00 2691 143 0.1641 0.1832 REMARK 3 4 3.0892 - 2.8069 1.00 2684 140 0.1920 0.1920 REMARK 3 5 2.8069 - 2.6058 0.99 2645 141 0.1877 0.2196 REMARK 3 6 2.6058 - 2.4522 1.00 2628 139 0.1854 0.1974 REMARK 3 7 2.4522 - 2.3294 1.00 2671 139 0.1716 0.2081 REMARK 3 8 2.3294 - 2.2280 1.00 2616 137 0.1730 0.2118 REMARK 3 9 2.2280 - 2.1423 1.00 2640 140 0.1764 0.2271 REMARK 3 10 2.1423 - 2.0684 0.99 2605 139 0.1810 0.2098 REMARK 3 11 2.0684 - 2.0037 0.99 2617 139 0.1868 0.2385 REMARK 3 12 2.0037 - 1.9464 0.98 2605 138 0.1927 0.2301 REMARK 3 13 1.9464 - 1.8952 0.95 2463 127 0.2100 0.2539 REMARK 3 14 1.8952 - 1.8490 0.81 2134 121 0.2189 0.2331 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.830 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 : 0.010 3188 REMARK 3 ANGLE : 1.134 4422 REMARK 3 CHIRALITY : 0.059 484 REMARK 3 PLANARITY : 0.007 515 REMARK 3 DIHEDRAL : 10.060 1645 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): 12.8074 -18.6417 -14.6218 REMARK 3 T TENSOR REMARK 3 T11: 0.1445 T22: 0.1515 REMARK 3 T33: 0.1365 T12: 0.0419 REMARK 3 T13: -0.0062 T23: -0.0326 REMARK 3 L TENSOR REMARK 3 L11: 1.4771 L22: 1.3553 REMARK 3 L33: 1.8146 L12: -0.3776 REMARK 3 L13: 0.2586 L23: -0.2818 REMARK 3 S TENSOR REMARK 3 S11: 0.0574 S12: 0.2069 S13: -0.1645 REMARK 3 S21: -0.1175 S22: -0.1095 S23: -0.1083 REMARK 3 S31: 0.1668 S32: 0.2805 S33: 0.0050 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESID 232:289 REMARK 3 ORIGIN FOR THE GROUP (A): 17.0991 8.0063 -16.9767 REMARK 3 T TENSOR REMARK 3 T11: 0.2175 T22: 0.2295 REMARK 3 T33: 0.2812 T12: -0.0021 REMARK 3 T13: 0.0650 T23: 0.0598 REMARK 3 L TENSOR REMARK 3 L11: 0.5718 L22: 0.6653 REMARK 3 L33: 0.7858 L12: -0.0104 REMARK 3 L13: -0.3126 L23: 0.5933 REMARK 3 S TENSOR REMARK 3 S11: 0.1110 S12: 0.1839 S13: 0.3204 REMARK 3 S21: -0.2501 S22: 0.0146 S23: -0.3072 REMARK 3 S31: -0.2529 S32: 0.1476 S33: 0.0019 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESID 290:423 REMARK 3 ORIGIN FOR THE GROUP (A): -1.8579 8.5840 -0.6863 REMARK 3 T TENSOR REMARK 3 T11: 0.1352 T22: 0.1107 REMARK 3 T33: 0.1415 T12: -0.0063 REMARK 3 T13: 0.0196 T23: -0.0272 REMARK 3 L TENSOR REMARK 3 L11: 1.9539 L22: 2.0870 REMARK 3 L33: 0.5666 L12: 0.2322 REMARK 3 L13: -0.3791 L23: 0.2199 REMARK 3 S TENSOR REMARK 3 S11: 0.1044 S12: -0.1549 S13: 0.4210 REMARK 3 S21: 0.1307 S22: -0.0610 S23: -0.1107 REMARK 3 S31: -0.1279 S32: -0.0203 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND RESID 424:494 REMARK 3 ORIGIN FOR THE GROUP (A): -11.1558 -10.2581 -11.4257 REMARK 3 T TENSOR REMARK 3 T11: 0.0933 T22: 0.1363 REMARK 3 T33: 0.0956 T12: 0.0037 REMARK 3 T13: -0.0185 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 1.0073 L22: 1.5980 REMARK 3 L33: 1.1757 L12: 0.0188 REMARK 3 L13: -0.6573 L23: 0.2822 REMARK 3 S TENSOR REMARK 3 S11: 0.0524 S12: 0.2804 S13: -0.1199 REMARK 3 S21: -0.0954 S22: -0.0744 S23: 0.2353 REMARK 3 S31: 0.0075 S32: -0.2546 S33: -0.0102 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 0.2706 -8.9584 -23.3811 REMARK 3 T TENSOR REMARK 3 T11: 0.1939 T22: 0.2521 REMARK 3 T33: 0.0637 T12: 0.0025 REMARK 3 T13: -0.0264 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 1.3927 L22: 0.3545 REMARK 3 L33: 0.6866 L12: 0.2008 REMARK 3 L13: -0.1408 L23: -0.4272 REMARK 3 S TENSOR REMARK 3 S11: 0.0360 S12: 0.4337 S13: -0.0264 REMARK 3 S21: -0.3229 S22: -0.0194 S23: 0.1186 REMARK 3 S31: 0.0424 S32: -0.1840 S33: 0.5118 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 5VZG 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_1000228191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39094 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.540 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 (%): 56.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 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 29.83400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.05400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.27750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.05400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.83400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.27750 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: 5160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 LEU A 196 CD1 CD2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 ARG A 211 NE CZ NH1 NH2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 LYS A 249 NZ 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 LEU A 280 CD1 CD2 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 GLN A 357 OE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 465 CD OE1 OE2 REMARK 470 GLN A 466 OE1 NE2 REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLN A 471 CD OE1 NE2 REMARK 470 GLU A 485 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC T 1 O3' DC T 1 C3' -0.038 REMARK 500 DT P 3 O3' DT P 3 C3' -0.058 REMARK 500 DG D 1 P DG D 1 OP3 -0.127 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. = -3.1 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 1.8 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 HIS A 151 -159.97 -150.91 REMARK 500 ASN A 153 39.86 -142.53 REMARK 500 THR A 318 -157.50 -126.86 REMARK 500 THR A 318 -151.17 -128.53 REMARK 500 SER A 411 -144.24 -166.58 REMARK 500 ASN A 493 49.49 -83.42 REMARK 500 REMARK 500 REMARK: NULL 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 97.2 REMARK 620 3 VAL A 246 O 90.5 94.1 REMARK 620 4 DT P 3 OP1 168.1 94.2 91.8 REMARK 620 5 HOH P 109 O 85.9 175.8 83.2 82.8 REMARK 620 6 HOH P 113 O 91.2 94.8 170.6 84.8 87.8 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 96.9 REMARK 620 3 ASP A 418 OD2 86.5 98.4 REMARK 620 4 2KH A 701 O2A 91.5 89.9 171.7 REMARK 620 5 HOH A 826 O 90.2 170.6 88.2 83.7 REMARK 620 6 DA P 4 O3' 172.0 84.4 85.5 96.4 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 91.2 REMARK 620 3 2KH A 701 O2A 98.7 91.4 REMARK 620 4 2KH A 701 O1B 170.4 93.8 89.4 REMARK 620 5 2KH A 701 O3G 87.1 177.2 91.1 87.6 REMARK 620 6 HOH A 871 O 80.8 84.0 175.4 91.5 93.5 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 CL A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 708 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 5VZG A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 5VZG T 1 9 PDB 5VZG 5VZG 1 9 DBREF 5VZG P 1 4 PDB 5VZG 5VZG 1 4 DBREF 5VZG D 1 4 PDB 5VZG 5VZG 1 4 SEQADV 5VZG GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZG SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZG ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZG ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZG ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 5VZG A UNP Q9NP87 PRO 398 DELETION SEQADV 5VZG A UNP Q9NP87 GLY 399 DELETION SEQADV 5VZG A UNP Q9NP87 ALA 400 DELETION SEQADV 5VZG A UNP Q9NP87 ALA 401 DELETION SEQADV 5VZG A UNP Q9NP87 VAL 402 DELETION SEQADV 5VZG A UNP Q9NP87 GLY 403 DELETION SEQADV 5VZG A UNP Q9NP87 GLY 404 DELETION SEQADV 5VZG A UNP Q9NP87 SER 405 DELETION SEQADV 5VZG A UNP Q9NP87 THR 406 DELETION SEQADV 5VZG A UNP Q9NP87 ARG 407 DELETION SEQADV 5VZG A UNP Q9NP87 PRO 408 DELETION SEQADV 5VZG A UNP Q9NP87 CYS 409 DELETION SEQADV 5VZG GLY A 410 UNP Q9NP87 PRO 410 LINKER SEQADV 5VZG HIS 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 HIS 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 CL A 706 1 HET EDO A 707 4 HET EDO A 708 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 CL CHLORIDE 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 CL 2(CL 1-) FORMUL 11 EDO 2(C2 H6 O2) FORMUL 13 HOH *295(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 GLN A 268 1 8 HELIX 10 AB1 PRO A 269 LEU A 272 5 4 HELIX 11 AB2 THR A 273 HIS A 282 1 10 HELIX 12 AB3 HIS A 282 SER A 287 1 6 HELIX 13 AB4 ARG A 292 LEU A 310 1 19 HELIX 14 AB5 GLY A 319 ARG A 323 1 5 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 THR A 318 0 SHEET 2 AA2 5 VAL A 331 THR A 336 -1 O ASP A 332 N THR A 318 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 2.43 LINK O ILE A 243 NA NA A 704 1555 1555 2.37 LINK O VAL A 246 NA NA A 704 1555 1555 2.29 LINK OD2 ASP A 330 MG MG A 702 1555 1555 2.02 LINK OD1 ASP A 330 MG MG A 703 1555 1555 2.03 LINK OD1 ASP A 332 MG MG A 702 1555 1555 2.06 LINK OD2 ASP A 332 MG MG A 703 1555 1555 2.07 LINK OD2 ASP A 418 MG MG A 702 1555 1555 2.09 LINK O2A 2KH A 701 MG MG A 702 1555 1555 2.29 LINK O2A 2KH A 701 MG MG A 703 1555 1555 2.13 LINK O1B 2KH A 701 MG MG A 703 1555 1555 2.02 LINK O3G 2KH A 701 MG MG A 703 1555 1555 2.14 LINK MG MG A 702 O HOH A 826 1555 1555 2.17 LINK MG MG A 702 O3'A DA P 4 1555 1555 2.10 LINK MG MG A 703 O HOH A 871 1555 1555 2.19 LINK NA NA A 704 OP1 DT P 3 1555 1555 2.55 LINK NA NA A 704 O HOH P 109 1555 1555 2.52 LINK NA NA A 704 O HOH P 113 1555 1555 2.51 CISPEP 1 GLY A 436 SER A 437 0 -3.60 SITE 1 AC1 26 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC1 26 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC1 26 GLY A 433 HIS A 434 GLY A 436 LYS A 438 SITE 4 AC1 26 MG A 702 MG A 703 EDO A 707 HOH A 807 SITE 5 AC1 26 HOH A 826 HOH A 852 HOH A 871 HOH A 874 SITE 6 AC1 26 HOH A 899 HOH A 905 HOH A 909 HOH A 927 SITE 7 AC1 26 DA P 4 DA T 5 SITE 1 AC2 7 ASP A 330 ASP A 332 ASP A 418 2KH A 701 SITE 2 AC2 7 MG A 703 HOH A 826 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 871 SITE 1 AC4 6 THR A 241 ILE A 243 VAL A 246 DT P 3 SITE 2 AC4 6 HOH P 109 HOH P 113 SITE 1 AC5 4 ASN A 457 SER A 458 EDO A 707 DA T 7 SITE 1 AC6 5 ARG A 387 HIS A 434 SER A 458 HOH A 813 SITE 2 AC6 5 HOH A 986 SITE 1 AC7 9 ARG A 387 GLY A 433 HIS A 434 ARG A 445 SITE 2 AC7 9 SER A 458 2KH A 701 CL A 705 DA P 4 SITE 3 AC7 9 DT T 6 SITE 1 AC8 4 PRO A 190 SER A 191 PRO A 192 GLN A 198 CRYST1 59.668 68.555 110.108 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 0.016759 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014587 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009082 0.00000