HEADER TRANSFERASE 20-MAY-19 6P1M TITLE BINARY COMPLEX OF HUMAN DNA POLYMERASE MU WITH 1-NT GAPPED SUBSTRATE TITLE 2 CONTAINING TEMPLATE 8OG 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 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*CP*GP*TP*A)-3'); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 17 CHAIN: D; COMPND 18 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_VARIANT: ROSETTA2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606 KEYWDS FAMILY X POLYMERASE, NHEJ, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.KAMINSKI,L.C.PEDERSEN,K.BEBENEK,K.K.CHIRUVELLA,D.A.RAMSDEN, AUTHOR 2 T.A.KUNKEL REVDAT 4 11-OCT-23 6P1M 1 LINK REVDAT 3 18-DEC-19 6P1M 1 REMARK REVDAT 2 09-OCT-19 6P1M 1 JRNL REVDAT 1 04-SEP-19 6P1M 0 JRNL AUTH A.M.KAMINSKI,K.K.CHIRUVELLA,D.A.RAMSDEN,T.A.KUNKEL, JRNL AUTH 2 K.BEBENEK,L.C.PEDERSEN JRNL TITL UNEXPECTED BEHAVIOR OF DNA POLYMERASE MU OPPOSITE TEMPLATE JRNL TITL 2 8-OXO-7,8-DIHYDRO-2'-GUANOSINE. JRNL REF NUCLEIC ACIDS RES. V. 47 9410 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 31435651 JRNL DOI 10.1093/NAR/GKZ680 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 55124 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 : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2755 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 26.1302 - 4.4697 0.99 2818 146 0.1665 0.2168 REMARK 3 2 4.4697 - 3.5506 1.00 2685 144 0.1393 0.1500 REMARK 3 3 3.5506 - 3.1026 1.00 2658 137 0.1628 0.1729 REMARK 3 4 3.1026 - 2.8193 1.00 2649 143 0.1859 0.1863 REMARK 3 5 2.8193 - 2.6174 1.00 2640 139 0.1798 0.1936 REMARK 3 6 2.6174 - 2.4632 1.00 2631 135 0.1709 0.1972 REMARK 3 7 2.4632 - 2.3399 1.00 2629 143 0.1672 0.2015 REMARK 3 8 2.3399 - 2.2381 1.00 2608 132 0.1659 0.2061 REMARK 3 9 2.2381 - 2.1520 1.00 2615 138 0.1595 0.1925 REMARK 3 10 2.1520 - 2.0778 1.00 2603 140 0.1565 0.1562 REMARK 3 11 2.0778 - 2.0128 1.00 2603 137 0.1608 0.1841 REMARK 3 12 2.0128 - 1.9553 1.00 2614 140 0.1669 0.2117 REMARK 3 13 1.9553 - 1.9039 1.00 2601 130 0.1705 0.2306 REMARK 3 14 1.9039 - 1.8574 1.00 2604 142 0.1710 0.1931 REMARK 3 15 1.8574 - 1.8152 1.00 2563 135 0.1683 0.2005 REMARK 3 16 1.8152 - 1.7766 1.00 2623 138 0.1647 0.1626 REMARK 3 17 1.7766 - 1.7411 1.00 2604 136 0.1725 0.2235 REMARK 3 18 1.7411 - 1.7082 1.00 2564 136 0.1773 0.2152 REMARK 3 19 1.7082 - 1.6777 1.00 2602 135 0.1990 0.2256 REMARK 3 20 1.6777 - 1.6493 0.95 2455 129 0.2247 0.2489 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.430 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 3112 REMARK 3 ANGLE : 1.064 4298 REMARK 3 CHIRALITY : 0.057 470 REMARK 3 PLANARITY : 0.008 510 REMARK 3 DIHEDRAL : 12.033 1018 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): 12.9143 -18.3020 -14.4470 REMARK 3 T TENSOR REMARK 3 T11: 0.1655 T22: 0.1593 REMARK 3 T33: 0.1669 T12: 0.0281 REMARK 3 T13: -0.0059 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 1.0893 L22: 0.6142 REMARK 3 L33: 0.6244 L12: -0.2405 REMARK 3 L13: 0.0687 L23: -0.1982 REMARK 3 S TENSOR REMARK 3 S11: 0.0025 S12: 0.0654 S13: -0.1147 REMARK 3 S21: -0.0270 S22: -0.0468 S23: -0.0793 REMARK 3 S31: 0.1238 S32: 0.1496 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 232:289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9098 8.2525 -16.9509 REMARK 3 T TENSOR REMARK 3 T11: 0.1870 T22: 0.1983 REMARK 3 T33: 0.2216 T12: -0.0187 REMARK 3 T13: 0.0258 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.0961 L22: 0.5827 REMARK 3 L33: 0.3839 L12: 0.0022 REMARK 3 L13: 0.0714 L23: 0.0856 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: 0.0427 S13: 0.0839 REMARK 3 S21: -0.0926 S22: -0.0485 S23: -0.1512 REMARK 3 S31: -0.1155 S32: 0.0512 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 290:423 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2412 8.4087 -0.1130 REMARK 3 T TENSOR REMARK 3 T11: 0.1440 T22: 0.1329 REMARK 3 T33: 0.1581 T12: 0.0031 REMARK 3 T13: -0.0025 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 0.8241 L22: 0.8058 REMARK 3 L33: 0.2782 L12: 0.0773 REMARK 3 L13: -0.4043 L23: -0.0695 REMARK 3 S TENSOR REMARK 3 S11: 0.0484 S12: -0.1049 S13: 0.1287 REMARK 3 S21: 0.1422 S22: -0.0360 S23: -0.0630 REMARK 3 S31: -0.0481 S32: 0.0274 S33: 0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 424:494 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7852 -10.0891 -11.1568 REMARK 3 T TENSOR REMARK 3 T11: 0.1302 T22: 0.1490 REMARK 3 T33: 0.1369 T12: -0.0085 REMARK 3 T13: -0.0097 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 0.5096 L22: 0.7478 REMARK 3 L33: 0.9401 L12: -0.0727 REMARK 3 L13: -0.4762 L23: 0.0657 REMARK 3 S TENSOR REMARK 3 S11: -0.0041 S12: 0.1005 S13: -0.0688 REMARK 3 S21: -0.0040 S22: -0.0293 S23: 0.0999 REMARK 3 S31: 0.0131 S32: -0.1458 S33: -0.0003 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN P AND RESID 1:4 ) OR ( CHAIN T AND RESID 1:9 REMARK 3 ) OR ( CHAIN D AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.2444 -7.1213 -23.1610 REMARK 3 T TENSOR REMARK 3 T11: 0.1981 T22: 0.2161 REMARK 3 T33: 0.1405 T12: 0.0053 REMARK 3 T13: -0.0227 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 0.1154 L22: 0.3868 REMARK 3 L33: 0.3215 L12: 0.1487 REMARK 3 L13: 0.0492 L23: -0.1807 REMARK 3 S TENSOR REMARK 3 S11: 0.0235 S12: 0.1551 S13: 0.0195 REMARK 3 S21: -0.1514 S22: -0.0142 S23: 0.0387 REMARK 3 S31: 0.0019 S32: -0.0459 S33: 0.0078 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 6P1M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55216 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 : 9.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.130 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 (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 92MM BIS-TRIS PH 6.5, 0.276M KBR, REMARK 280 20.7% W/V POLYPURE PEGS 0.3-8KDA, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 29.96450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.20650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.13150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.20650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.96450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.13150 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: 6570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 HIS A 365 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 465 ALA A 384 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 158 CD OE1 OE2 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 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 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 300 CD OE1 NE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 OE1 NE2 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 PHE A 385 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 394 CD1 CD2 REMARK 470 GLU A 465 CD OE1 OE2 REMARK 470 LYS A 467 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: 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' -0.036 REMARK 500 DG D 1 P DG D 1 OP3 -0.119 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 393 NE - CZ - NH2 ANGL. DEV. = -3.1 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 -159.84 -154.40 REMARK 500 ASN A 153 40.08 -140.43 REMARK 500 LEU A 310 96.49 -160.92 REMARK 500 THR A 318 -149.58 -122.18 REMARK 500 THR A 318 -157.13 -132.95 REMARK 500 PRO A 397 108.90 -50.13 REMARK 500 SER A 411 -139.41 -165.16 REMARK 500 ASN A 493 49.60 -86.57 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 A 912 DISTANCE = 5.90 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 K A 502 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 93.5 REMARK 620 3 VAL A 246 O 84.3 80.5 REMARK 620 4 HOH A 803 O 93.8 76.6 156.8 REMARK 620 5 DT P 3 OP1 173.3 87.1 89.2 92.9 REMARK 620 6 HOH P 113 O 97.8 137.6 141.1 62.1 86.2 REMARK 620 7 HOH P 114 O 89.6 156.9 77.1 126.0 87.3 64.1 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 BR A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO2 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 512 DBREF 6P1M A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 6P1M T 1 9 PDB 6P1M 6P1M 1 9 DBREF 6P1M P 1 4 PDB 6P1M 6P1M 1 4 DBREF 6P1M D 1 4 PDB 6P1M 6P1M 1 4 SEQADV 6P1M GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1M SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1M ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1M ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1M ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1M A UNP Q9NP87 PRO 398 DELETION SEQADV 6P1M A UNP Q9NP87 GLY 399 DELETION SEQADV 6P1M A UNP Q9NP87 ALA 400 DELETION SEQADV 6P1M A UNP Q9NP87 ALA 401 DELETION SEQADV 6P1M A UNP Q9NP87 VAL 402 DELETION SEQADV 6P1M A UNP Q9NP87 GLY 403 DELETION SEQADV 6P1M A UNP Q9NP87 GLY 404 DELETION SEQADV 6P1M A UNP Q9NP87 SER 405 DELETION SEQADV 6P1M A UNP Q9NP87 THR 406 DELETION SEQADV 6P1M A UNP Q9NP87 ARG 407 DELETION SEQADV 6P1M A UNP Q9NP87 PRO 408 DELETION SEQADV 6P1M A UNP Q9NP87 CYS 409 DELETION SEQADV 6P1M GLY A 410 UNP Q9NP87 PRO 410 LINKER 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 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 8OG DT DA DC DG SEQRES 1 P 4 DC DG DT DA SEQRES 1 D 4 DG DC DC DG HET 8OG T 5 23 HET BR A 501 1 HET K A 502 1 HET CL A 503 1 HET BR A 504 1 HET CL A 505 1 HET CO2 A 506 3 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 509 4 HET EDO A 510 4 HET EDO A 511 4 HET EDO A 512 4 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM BR BROMIDE ION HETNAM K POTASSIUM ION HETNAM CL CHLORIDE ION HETNAM CO2 CARBON DIOXIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 5 BR 2(BR 1-) FORMUL 6 K K 1+ FORMUL 7 CL 2(CL 1-) FORMUL 10 CO2 C O2 FORMUL 11 EDO 6(C2 H6 O2) FORMUL 17 HOH *390(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 ASP A 330 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 LEU A 456 0 SHEET 2 AA3 3 LEU A 461 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 O3' DC T 4 P 8OG T 5 1555 1555 1.60 LINK O3' 8OG T 5 P DT T 6 1555 1555 1.61 LINK O THR A 241 K K A 502 1555 1555 2.67 LINK O ILE A 243 K K A 502 1555 1555 2.73 LINK O VAL A 246 K K A 502 1555 1555 2.64 LINK K K A 502 O HOH A 803 1555 1555 3.09 LINK K K A 502 OP1 DT P 3 1555 1555 2.75 LINK K K A 502 O HOH P 113 1555 1555 3.14 LINK K K A 502 O HOH P 114 1555 1555 2.79 CISPEP 1 GLY A 436 SER A 437 0 -1.60 SITE 1 AC1 3 SER A 474 GLU A 475 HOH A 770 SITE 1 AC2 6 THR A 241 ILE A 243 VAL A 246 HOH A 803 SITE 2 AC2 6 DT P 3 HOH P 114 SITE 1 AC3 3 SER A 172 GLY A 174 ARG A 175 SITE 1 AC4 4 ARG A 387 ARG A 445 SER A 458 DA T 7 SITE 1 AC5 3 ARG A 446 HOH A 659 HOH T 116 SITE 1 AC6 4 LYS A 325 LEU A 326 GLN A 327 HOH A 784 SITE 1 AC7 4 PRO A 289 LYS A 325 GLN A 327 HIS A 329 SITE 1 AC8 5 THR A 154 GLY A 155 GLU A 476 HOH A 602 SITE 2 AC8 5 HOH A 671 SITE 1 AC9 5 ARG A 292 THR A 316 LEU A 317 ARG A 322 SITE 2 AC9 5 HOH A 691 SITE 1 AD1 7 GLY A 433 TRP A 434 GLN A 441 ARG A 445 SITE 2 AD1 7 SER A 458 HOH A 724 DA P 4 SITE 1 AD2 3 LYS A 438 ARG A 442 HOH A 726 SITE 1 AD3 1 THR A 314 CRYST1 59.929 68.263 110.413 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 0.016686 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014649 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009057 0.00000