HEADER TRANSFERASE 20-MAY-19 6P1O TITLE POST-CATALYTIC NICKED COMPLEX OF HUMAN DNA POLYMERASE MU WITH 1-NT TITLE 2 GAPPED SUBSTRATE CONTAINING TEMPLATE 8OG AND NEWLY INCORPORATED DAMP 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*AP*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 6P1O 1 LINK REVDAT 3 18-DEC-19 6P1O 1 REMARK REVDAT 2 09-OCT-19 6P1O 1 JRNL REVDAT 1 04-SEP-19 6P1O 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) : 25.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 53396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2690 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 25.1503 - 4.3945 1.00 2997 156 0.1689 0.1857 REMARK 3 2 4.3945 - 3.4910 1.00 2853 152 0.1414 0.1482 REMARK 3 3 3.4910 - 3.0506 1.00 2831 147 0.1616 0.1668 REMARK 3 4 3.0506 - 2.7721 1.00 2795 149 0.1914 0.1986 REMARK 3 5 2.7721 - 2.5736 1.00 2798 146 0.1896 0.1997 REMARK 3 6 2.5736 - 2.4220 1.00 2778 148 0.1768 0.2252 REMARK 3 7 2.4220 - 2.3008 1.00 2779 148 0.1674 0.1859 REMARK 3 8 2.3008 - 2.2007 1.00 2794 145 0.1706 0.2059 REMARK 3 9 2.2007 - 2.1160 0.99 2727 139 0.1614 0.1903 REMARK 3 10 2.1160 - 2.0430 0.98 2734 149 0.1621 0.1845 REMARK 3 11 2.0430 - 1.9792 0.97 2670 138 0.1609 0.2111 REMARK 3 12 1.9792 - 1.9226 0.95 2653 137 0.1734 0.2087 REMARK 3 13 1.9226 - 1.8720 0.94 2591 140 0.1718 0.2040 REMARK 3 14 1.8720 - 1.8264 0.92 2529 134 0.1792 0.1916 REMARK 3 15 1.8264 - 1.7849 0.92 2539 136 0.1726 0.1933 REMARK 3 16 1.7849 - 1.7469 0.90 2467 137 0.1803 0.2154 REMARK 3 17 1.7469 - 1.7120 0.89 2436 132 0.1687 0.2311 REMARK 3 18 1.7120 - 1.6797 0.87 2405 126 0.1826 0.2055 REMARK 3 19 1.6797 - 1.6497 0.86 2330 131 0.1847 0.2440 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) : 18.250 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 : 0.008 3163 REMARK 3 ANGLE : 1.030 4388 REMARK 3 CHIRALITY : 0.057 478 REMARK 3 PLANARITY : 0.007 513 REMARK 3 DIHEDRAL : 9.356 1652 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): 12.7340 -18.6565 -14.5000 REMARK 3 T TENSOR REMARK 3 T11: 0.2021 T22: 0.2032 REMARK 3 T33: 0.1917 T12: 0.0368 REMARK 3 T13: -0.0020 T23: -0.0197 REMARK 3 L TENSOR REMARK 3 L11: 0.8055 L22: 0.9094 REMARK 3 L33: 0.7249 L12: -0.2630 REMARK 3 L13: 0.1671 L23: -0.1640 REMARK 3 S TENSOR REMARK 3 S11: 0.0384 S12: 0.1210 S13: -0.1180 REMARK 3 S21: -0.0583 S22: -0.0788 S23: -0.0555 REMARK 3 S31: 0.1348 S32: 0.1651 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 232:289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0848 8.2585 -17.1650 REMARK 3 T TENSOR REMARK 3 T11: 0.2237 T22: 0.2355 REMARK 3 T33: 0.2822 T12: -0.0058 REMARK 3 T13: 0.0599 T23: 0.0467 REMARK 3 L TENSOR REMARK 3 L11: 0.3561 L22: 0.6753 REMARK 3 L33: 0.2588 L12: -0.0222 REMARK 3 L13: 0.1567 L23: 0.2513 REMARK 3 S TENSOR REMARK 3 S11: 0.0562 S12: 0.0917 S13: 0.1900 REMARK 3 S21: -0.1714 S22: -0.0127 S23: -0.2492 REMARK 3 S31: -0.2189 S32: 0.0968 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 290:423 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0251 8.6326 -0.4419 REMARK 3 T TENSOR REMARK 3 T11: 0.1794 T22: 0.1660 REMARK 3 T33: 0.1890 T12: -0.0016 REMARK 3 T13: 0.0112 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 1.2243 L22: 0.9057 REMARK 3 L33: 0.0381 L12: 0.0376 REMARK 3 L13: -0.1340 L23: -0.1164 REMARK 3 S TENSOR REMARK 3 S11: 0.0824 S12: -0.0992 S13: 0.2269 REMARK 3 S21: 0.1037 S22: -0.0464 S23: -0.0625 REMARK 3 S31: -0.0392 S32: -0.0332 S33: 0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 424:494 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.1252 -10.3629 -11.3441 REMARK 3 T TENSOR REMARK 3 T11: 0.1663 T22: 0.1917 REMARK 3 T33: 0.1695 T12: -0.0053 REMARK 3 T13: -0.0066 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.6984 L22: 0.8454 REMARK 3 L33: 1.0264 L12: -0.0360 REMARK 3 L13: -0.3871 L23: 0.3016 REMARK 3 S TENSOR REMARK 3 S11: 0.0045 S12: 0.1385 S13: -0.0445 REMARK 3 S21: -0.0145 S22: -0.0435 S23: 0.1050 REMARK 3 S31: 0.0230 S32: -0.1622 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN P AND RESID 1:5 ) OR ( CHAIN T AND RESID 1:9 REMARK 3 ) OR ( CHAIN D AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.3189 -6.9024 -22.4874 REMARK 3 T TENSOR REMARK 3 T11: 0.2293 T22: 0.2562 REMARK 3 T33: 0.1578 T12: 0.0120 REMARK 3 T13: -0.0064 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 0.3274 L22: 0.5720 REMARK 3 L33: 0.2980 L12: 0.3239 REMARK 3 L13: 0.1431 L23: -0.1167 REMARK 3 S TENSOR REMARK 3 S11: 0.0487 S12: 0.2089 S13: 0.0551 REMARK 3 S21: -0.1256 S22: -0.0259 S23: 0.0438 REMARK 3 S31: -0.0091 S32: -0.0710 S33: 0.0095 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 6P1O 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_1000241713. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-15 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) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : VARIMAX-HF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53497 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 (%) : 95.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 47.9000 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) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39500 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 (%): 57.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.5, 100MM NACL, 10% REMARK 280 W/V PEG4000, VAPOR DIFFUSION, SITTING DROP, 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 29.97350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.36200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.35650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.36200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.97350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.35650 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: 6750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 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 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 173 CD OE1 OE2 REMARK 470 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 GLN A 242 CD OE1 NE2 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 OD1 OD2 REMARK 470 GLN A 300 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 HIS A 363 ND1 CD2 CE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 465 CD OE1 OE2 REMARK 470 GLN A 466 CD OE1 NE2 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: 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' -0.043 REMARK 500 DT T 6 O3' DT T 6 C3' -0.039 REMARK 500 DG D 1 P DG D 1 OP3 -0.118 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 DT T 6 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT P 3 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 ASN A 153 40.51 -141.48 REMARK 500 THR A 318 -153.82 -124.94 REMARK 500 THR A 318 -152.63 -128.70 REMARK 500 SER A 411 -145.05 -162.84 REMARK 500 SER A 437 172.16 -58.85 REMARK 500 ASN A 493 47.79 -84.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE AUTHORS STATE THAT ANOMALOUS SIGNAL IS OBSERVED FOR THE METAL A REMARK 600 SITE (PEAK GREATER THAN 10 SIGMA), THOUGH NO ANOMALOUS SCATTERERS REMARK 600 WERE ADDED TO THE CRYSTALLIZATION OR SOAKING SOLUTIONS. THEREFORE, REMARK 600 THIS METAL HAS BEEN MODELED AS MANGANESE, BASED ON THE COORDINATION REMARK 600 GEOMETRY AND INTERATOMIC DISTANCES. 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 509 REMARK 610 ATP P 701 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 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 98.5 REMARK 620 3 VAL A 246 O 93.9 92.2 REMARK 620 4 HOH A 830 O 88.0 85.5 177.2 REMARK 620 5 DT P 3 OP1 173.5 86.5 89.9 88.3 REMARK 620 6 HOH P 812 O 91.5 169.1 91.4 90.6 83.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 120.9 REMARK 620 3 ASP A 418 OD2 93.8 103.0 REMARK 620 4 DA P 5 OP1 105.2 103.1 132.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 94.3 REMARK 620 3 PPV A 507 O32 88.1 169.4 REMARK 620 4 PPV A 507 O11 165.8 95.7 83.8 REMARK 620 5 HOH A 745 O 83.2 88.4 102.2 87.1 REMARK 620 6 DA P 5 OP1 87.7 85.2 84.6 103.2 168.4 REMARK 620 7 ATP P 701 O2B 86.4 171.4 2.4 85.1 100.2 86.3 REMARK 620 8 ATP P 701 O2G 165.3 100.0 78.3 8.0 94.0 96.7 79.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 CL A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV 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 EPE A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP P 701 DBREF 6P1O A 134 494 UNP Q9NP87 DPOLM_HUMAN 134 494 DBREF 6P1O T 1 9 PDB 6P1O 6P1O 1 9 DBREF 6P1O P 1 5 PDB 6P1O 6P1O 1 5 DBREF 6P1O D 1 4 PDB 6P1O 6P1O 1 4 SEQADV 6P1O GLY A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1O SER A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1O ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1O ALA A 132 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1O ALA A 133 UNP Q9NP87 EXPRESSION TAG SEQADV 6P1O A UNP Q9NP87 PRO 398 DELETION SEQADV 6P1O A UNP Q9NP87 GLY 399 DELETION SEQADV 6P1O A UNP Q9NP87 ALA 400 DELETION SEQADV 6P1O A UNP Q9NP87 ALA 401 DELETION SEQADV 6P1O A UNP Q9NP87 VAL 402 DELETION SEQADV 6P1O A UNP Q9NP87 GLY 403 DELETION SEQADV 6P1O A UNP Q9NP87 GLY 404 DELETION SEQADV 6P1O A UNP Q9NP87 SER 405 DELETION SEQADV 6P1O A UNP Q9NP87 THR 406 DELETION SEQADV 6P1O A UNP Q9NP87 ARG 407 DELETION SEQADV 6P1O A UNP Q9NP87 PRO 408 DELETION SEQADV 6P1O A UNP Q9NP87 CYS 409 DELETION SEQADV 6P1O 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 5 DC DG DT DA DA SEQRES 1 D 4 DG DC DC DG HET 8OG T 5 23 HET MN A 501 1 HET MG A 502 1 HET NA A 503 1 HET CL A 504 1 HET CL A 505 1 HET CL A 506 1 HET PPV A 507 9 HET EDO A 508 4 HET EPE A 509 5 HET ATP P 701 10 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PPV PYROPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 2 8OG C10 H14 N5 O8 P FORMUL 5 MN MN 2+ FORMUL 6 MG MG 2+ FORMUL 7 NA NA 1+ FORMUL 8 CL 3(CL 1-) FORMUL 11 PPV H4 O7 P2 FORMUL 12 EDO C2 H6 O2 FORMUL 13 EPE C8 H18 N2 O4 S FORMUL 14 ATP C10 H16 N5 O13 P3 FORMUL 15 HOH *353(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 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 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 NA NA A 503 1555 1555 2.26 LINK O ILE A 243 NA NA A 503 1555 1555 2.43 LINK O VAL A 246 NA NA A 503 1555 1555 2.22 LINK OD2 ASP A 330 MN MN A 501 1555 1555 1.83 LINK OD1 ASP A 330 MG MG A 502 1555 1555 2.20 LINK OD1 ASP A 332 MN MN A 501 1555 1555 1.82 LINK OD2 ASP A 332 MG MG A 502 1555 1555 2.17 LINK OD2 ASP A 418 MN MN A 501 1555 1555 1.99 LINK MN MN A 501 OP1 DA P 5 1555 1555 2.14 LINK MG MG A 502 O32APPV A 507 1555 1555 2.30 LINK MG MG A 502 O11APPV A 507 1555 1555 2.24 LINK MG MG A 502 O HOH A 745 1555 1555 2.31 LINK MG MG A 502 OP1 DA P 5 1555 1555 2.45 LINK MG MG A 502 O2BBATP P 701 1555 1555 2.40 LINK MG MG A 502 O2GBATP P 701 1555 1555 2.02 LINK NA NA A 503 O HOH A 830 1555 1555 2.47 LINK NA NA A 503 OP1 DT P 3 1555 1555 2.73 LINK NA NA A 503 O HOH P 812 1555 1555 2.34 CISPEP 1 GLY A 436 SER A 437 0 -7.45 SITE 1 AC1 6 ASP A 330 ASP A 332 ASP A 418 MG A 502 SITE 2 AC1 6 DA P 4 DA P 5 SITE 1 AC2 7 ASP A 330 ASP A 332 MN A 501 PPV A 507 SITE 2 AC2 7 HOH A 745 DA P 5 ATP P 701 SITE 1 AC3 6 THR A 241 ILE A 243 VAL A 246 HOH A 830 SITE 2 AC3 6 DT P 3 HOH P 812 SITE 1 AC4 2 SER A 458 DA T 7 SITE 1 AC5 3 SER A 172 GLY A 174 ARG A 175 SITE 1 AC6 2 ARG A 393 HOH A 820 SITE 1 AC7 13 GLY A 319 GLY A 320 ARG A 323 HIS A 329 SITE 2 AC7 13 ASP A 330 ASP A 332 MG A 502 HOH A 601 SITE 3 AC7 13 HOH A 607 HOH A 614 HOH A 655 DA P 5 SITE 4 AC7 13 ATP P 701 SITE 1 AC8 5 ARG A 387 GLY A 433 ARG A 445 DA P 4 SITE 2 AC8 5 DA P 5 SITE 1 AC9 4 LYS A 325 LEU A 326 GLN A 327 HOH A 612 SITE 1 AD1 12 GLY A 320 ARG A 323 HIS A 329 ASP A 330 SITE 2 AD1 12 ASP A 332 MG A 502 PPV A 507 HOH A 601 SITE 3 AD1 12 HOH A 607 HOH A 614 HOH A 655 DA P 5 CRYST1 59.947 68.713 110.724 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 0.016681 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009031 0.00000