HEADER REPLICATION/DNA 24-NOV-20 7KSU TITLE DNA POLYMERASE MU, DGTP:CT PRODUCT STATE TERNARY COMPLEX, 10 MM MN2+ TITLE 2 (4MIN) 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*CP*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*G)-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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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: HOMO SAPIENS; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 MOL_ID: 4; SOURCE 19 SYNTHETIC: YES; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_TAXID: 9606 KEYWDS TIME-LAPSE CRYSTALLOGRAPHY, OXIDIZED NUCLEOTIDE INSERTION, DNA KEYWDS 2 POLYMERASE MU, DOUBLE STRAND BREAK REPAIR, REPLICATION, REPLICATION- KEYWDS 3 DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JAMSEN,S.H.WILSON REVDAT 2 18-OCT-23 7KSU 1 REMARK REVDAT 1 19-JAN-22 7KSU 0 JRNL AUTH J.A.JAMSEN,A.SASSA,D.D.SHOCK,W.A.BEARD,S.H.WILSON JRNL TITL WATCHING A DOUBLE STRAND BREAK REPAIR POLYMERASE INSERT A JRNL TITL 2 PRO-MUTAGENIC OXIDIZED NUCLEOTIDE. JRNL REF NAT COMMUN V. 12 2059 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33824325 JRNL DOI 10.1038/S41467-021-21354-6 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2-3472 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 54837 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2737 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 41.8230 - 4.4778 0.99 2804 146 0.1836 0.2128 REMARK 3 2 4.4778 - 3.5547 0.98 2654 140 0.1529 0.1540 REMARK 3 3 3.5547 - 3.1056 0.97 2602 140 0.1759 0.1889 REMARK 3 4 3.1056 - 2.8217 0.99 2639 133 0.1779 0.1885 REMARK 3 5 2.8217 - 2.6195 0.99 2618 141 0.1749 0.1857 REMARK 3 6 2.6195 - 2.4651 0.99 2595 138 0.1671 0.1757 REMARK 3 7 2.4651 - 2.3416 0.99 2617 138 0.1568 0.2000 REMARK 3 8 2.3416 - 2.2397 1.00 2604 137 0.1602 0.1666 REMARK 3 9 2.2397 - 2.1535 1.00 2602 139 0.1624 0.2032 REMARK 3 10 2.1535 - 2.0792 1.00 2621 133 0.1642 0.1759 REMARK 3 11 2.0792 - 2.0142 1.00 2610 141 0.1676 0.2038 REMARK 3 12 2.0142 - 1.9566 1.00 2610 138 0.1750 0.2100 REMARK 3 13 1.9566 - 1.9051 1.00 2603 140 0.1809 0.2023 REMARK 3 14 1.9051 - 1.8586 1.00 2595 132 0.1785 0.2283 REMARK 3 15 1.8586 - 1.8163 1.00 2611 136 0.1899 0.2068 REMARK 3 16 1.8163 - 1.7777 1.00 2602 137 0.1961 0.2341 REMARK 3 17 1.7777 - 1.7421 1.00 2602 138 0.2061 0.2221 REMARK 3 18 1.7421 - 1.7093 1.00 2573 135 0.2121 0.2452 REMARK 3 19 1.7093 - 1.6787 1.00 2590 137 0.2334 0.2543 REMARK 3 20 1.6787 - 1.6503 0.90 2348 118 0.2403 0.2628 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.42 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 3186 REMARK 3 ANGLE : 0.953 4410 REMARK 3 CHIRALITY : 0.056 478 REMARK 3 PLANARITY : 0.006 516 REMARK 3 DIHEDRAL : 13.683 1030 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 138 THROUGH 494) REMARK 3 ORIGIN FOR THE GROUP (A): 3.4976 -3.4140 -9.9535 REMARK 3 T TENSOR REMARK 3 T11: 0.2118 T22: 0.2138 REMARK 3 T33: 0.1795 T12: 0.0036 REMARK 3 T13: 0.0121 T23: 0.0185 REMARK 3 L TENSOR REMARK 3 L11: 1.7076 L22: 1.0913 REMARK 3 L33: 0.7104 L12: -0.4009 REMARK 3 L13: -0.1213 L23: 0.1679 REMARK 3 S TENSOR REMARK 3 S11: 0.0989 S12: 0.1190 S13: 0.1399 REMARK 3 S21: -0.0367 S22: -0.0574 S23: -0.1148 REMARK 3 S31: 0.0105 S32: 0.0433 S33: 0.0045 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'T' AND RESID 1 THROUGH 9) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0274 -6.1985 -24.2863 REMARK 3 T TENSOR REMARK 3 T11: 0.2957 T22: 0.3525 REMARK 3 T33: 0.1802 T12: 0.0549 REMARK 3 T13: -0.0265 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.5933 L22: 0.3634 REMARK 3 L33: 0.0485 L12: -0.1248 REMARK 3 L13: -0.0272 L23: -0.1207 REMARK 3 S TENSOR REMARK 3 S11: 0.2279 S12: 0.5647 S13: -0.0817 REMARK 3 S21: -0.5906 S22: -0.1613 S23: -0.0018 REMARK 3 S31: -0.1407 S32: -0.1581 S33: -0.0015 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'P' AND RESID 1 THROUGH 5) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4210 3.5520 -16.6040 REMARK 3 T TENSOR REMARK 3 T11: 0.2811 T22: 0.3047 REMARK 3 T33: 0.2389 T12: 0.0072 REMARK 3 T13: 0.0390 T23: 0.0823 REMARK 3 L TENSOR REMARK 3 L11: 0.0153 L22: 0.0248 REMARK 3 L33: 0.0289 L12: 0.0197 REMARK 3 L13: 0.0210 L23: 0.0269 REMARK 3 S TENSOR REMARK 3 S11: 0.1721 S12: 0.3780 S13: 0.1271 REMARK 3 S21: -0.1720 S22: -0.1181 S23: 0.0463 REMARK 3 S31: 0.0006 S32: 0.0418 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 1 THROUGH 4) REMARK 3 ORIGIN FOR THE GROUP (A): 4.7860 -21.0341 -25.7588 REMARK 3 T TENSOR REMARK 3 T11: 0.3597 T22: 0.4436 REMARK 3 T33: 0.2169 T12: 0.0072 REMARK 3 T13: -0.0642 T23: -0.1169 REMARK 3 L TENSOR REMARK 3 L11: 0.4562 L22: 0.8553 REMARK 3 L33: 0.1562 L12: -0.6056 REMARK 3 L13: 0.1953 L23: -0.3203 REMARK 3 S TENSOR REMARK 3 S11: 0.0834 S12: 0.0540 S13: -0.2127 REMARK 3 S21: -0.2752 S22: -0.1339 S23: 0.3160 REMARK 3 S31: 0.4787 S32: -0.5332 S33: 0.0354 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 7KSU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000252998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-18 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-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54904 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 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) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.97600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 4M04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85-90MM HEPES PH 7.5, 17-18% PEG 4000, REMARK 280 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 29.99250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.87350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.44100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.87350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.99250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.44100 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: 7020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 127 REMARK 465 SER A 128 REMARK 465 ALA A 129 REMARK 465 ALA A 130 REMARK 465 ALA A 131 REMARK 465 PRO A 132 REMARK 465 LEU 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 LEU A 196 CD1 CD2 REMARK 470 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 ARG A 211 CZ NH1 NH2 REMARK 470 GLU A 223 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 300 CD OE1 NE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 CD OE1 NE2 REMARK 470 ASP A 356 OD1 OD2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 GLN A 364 C O CB 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 CE NZ REMARK 470 GLN A 471 CD OE1 NE2 REMARK 470 GLU A 485 CG 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' -0.038 REMARK 500 DG D 1 P DG D 1 OP3 -0.126 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. = 1.9 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = 2.7 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 40.66 -141.92 REMARK 500 THR A 318 -150.79 -123.86 REMARK 500 THR A 318 -155.03 -127.73 REMARK 500 PRO A 397 105.93 -55.37 REMARK 500 SER A 411 -145.43 -165.02 REMARK 500 ASN A 493 47.07 -87.44 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 EDO A 509 REMARK 610 EPE A 513 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 MN A 504 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 208 ND1 REMARK 620 2 HOH A 810 O 103.5 REMARK 620 3 DG D 1 OP3 69.0 119.1 REMARK 620 4 HOH D 105 O 87.2 153.4 87.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 505 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 218 OE1 REMARK 620 2 HIS A 219 NE2 92.9 REMARK 620 3 HOH A 602 O 163.8 71.6 REMARK 620 4 HOH A 709 O 69.0 87.4 104.6 REMARK 620 5 HOH A 735 O 76.9 105.4 111.2 144.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 506 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 99.0 REMARK 620 3 VAL A 246 O 93.7 93.1 REMARK 620 4 HOH A 779 O 81.0 92.3 173.0 REMARK 620 5 DT P 3 OP1 171.2 88.7 90.0 94.6 REMARK 620 6 HOH P 213 O 89.4 171.4 88.3 87.0 82.8 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 98.6 REMARK 620 3 ASP A 418 OD2 99.2 94.5 REMARK 620 4 DA P 4 O3' 163.2 95.6 88.4 REMARK 620 5 DG P 5 OP1 110.5 90.4 148.8 60.5 REMARK 620 6 HOH P 201 O 85.5 171.2 92.6 79.2 80.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 95.4 REMARK 620 3 PPV A 507 O12 83.8 174.1 REMARK 620 4 PPV A 507 O32 88.4 166.5 19.4 REMARK 620 5 PPV A 507 O11 165.3 92.0 87.6 87.4 REMARK 620 6 PPV A 507 O21 162.6 98.4 81.3 80.7 6.8 REMARK 620 7 HOH A 699 O 81.3 84.1 90.0 109.4 86.8 89.5 REMARK 620 8 DG P 5 OP1 90.1 86.6 99.3 80.4 103.1 101.3 166.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 503 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 386 OE1 REMARK 620 2 GLU A 386 OE2 52.7 REMARK 620 3 HIS A 459 NE2 141.8 90.6 REMARK 620 4 HOH A 774 O 85.8 97.9 89.8 REMARK 620 5 HOH A 800 O 114.8 166.7 102.5 84.2 REMARK 620 6 HOH T 203 O 91.7 89.2 98.8 168.8 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN P 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PPV A 507 O22 REMARK 620 2 HOH A 778 O 91.4 REMARK 620 3 DG P 5 OP2 91.0 174.3 REMARK 620 4 HOH P 208 O 176.1 86.0 91.8 REMARK 620 5 HOH P 212 O 99.7 94.2 90.5 77.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN T 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG T 2 N7 REMARK 620 2 HOH T 201 O 88.5 REMARK 620 3 HOH T 205 O 86.4 84.4 REMARK 620 4 HOH T 224 O 94.4 80.5 164.8 REMARK 620 N 1 2 3 DBREF 7KSU A 127 494 UNP Q9NP87 DPOLM_HUMAN 127 494 DBREF 7KSU T 1 9 PDB 7KSU 7KSU 1 9 DBREF 7KSU P 1 5 PDB 7KSU 7KSU 1 5 DBREF 7KSU D 1 4 PDB 7KSU 7KSU 1 4 SEQADV 7KSU SER A 128 UNP Q9NP87 PRO 128 CONFLICT SEQADV 7KSU ALA A 129 UNP Q9NP87 ARG 129 CONFLICT SEQADV 7KSU ALA A 130 UNP Q9NP87 LYS 130 CONFLICT SEQADV 7KSU ALA A 131 UNP Q9NP87 GLY 131 CONFLICT SEQADV 7KSU A UNP Q9NP87 PRO 398 DELETION SEQADV 7KSU A UNP Q9NP87 GLY 399 DELETION SEQADV 7KSU A UNP Q9NP87 ALA 400 DELETION SEQADV 7KSU A UNP Q9NP87 ALA 401 DELETION SEQADV 7KSU A UNP Q9NP87 VAL 402 DELETION SEQADV 7KSU A UNP Q9NP87 GLY 403 DELETION SEQADV 7KSU A UNP Q9NP87 GLY 404 DELETION SEQADV 7KSU A UNP Q9NP87 SER 405 DELETION SEQADV 7KSU A UNP Q9NP87 THR 406 DELETION SEQADV 7KSU A UNP Q9NP87 ARG 407 DELETION SEQADV 7KSU A UNP Q9NP87 PRO 408 DELETION SEQADV 7KSU A UNP Q9NP87 CYS 409 DELETION SEQADV 7KSU GLY A 410 UNP Q9NP87 PRO 410 CONFLICT SEQRES 1 A 356 GLY SER ALA ALA ALA PRO LEU SER PRO ALA TRP MET PRO SEQRES 2 A 356 ALA TYR ALA CYS GLN ARG PRO THR PRO LEU THR HIS HIS SEQRES 3 A 356 ASN THR GLY LEU SER GLU ALA LEU GLU ILE LEU ALA GLU SEQRES 4 A 356 ALA ALA GLY PHE GLU GLY SER GLU GLY ARG LEU LEU THR SEQRES 5 A 356 PHE CYS ARG ALA ALA SER VAL LEU LYS ALA LEU PRO SER SEQRES 6 A 356 PRO VAL THR THR LEU SER GLN LEU GLN GLY LEU PRO HIS SEQRES 7 A 356 PHE GLY GLU HIS SER SER ARG VAL VAL GLN GLU LEU LEU SEQRES 8 A 356 GLU HIS GLY VAL CYS GLU GLU VAL GLU ARG VAL ARG ARG SEQRES 9 A 356 SER GLU ARG TYR GLN THR MET LYS LEU PHE THR GLN ILE SEQRES 10 A 356 PHE GLY VAL GLY VAL LYS THR ALA ASP ARG TRP TYR ARG SEQRES 11 A 356 GLU GLY LEU ARG THR LEU ASP ASP LEU ARG GLU GLN PRO SEQRES 12 A 356 GLN LYS LEU THR GLN GLN GLN LYS ALA GLY LEU GLN HIS SEQRES 13 A 356 HIS GLN ASP LEU SER THR PRO VAL LEU ARG SER ASP VAL SEQRES 14 A 356 ASP ALA LEU GLN GLN VAL VAL GLU GLU ALA VAL GLY GLN SEQRES 15 A 356 ALA LEU PRO GLY ALA THR VAL THR LEU THR GLY GLY PHE SEQRES 16 A 356 ARG ARG GLY LYS LEU GLN GLY HIS ASP VAL ASP PHE LEU SEQRES 17 A 356 ILE THR HIS PRO LYS GLU GLY GLN GLU ALA GLY LEU LEU SEQRES 18 A 356 PRO ARG VAL MET CYS ARG LEU GLN ASP GLN GLY LEU ILE SEQRES 19 A 356 LEU TYR HIS GLN HIS GLN HIS SER CYS CYS GLU SER PRO SEQRES 20 A 356 THR ARG LEU ALA GLN GLN SER HIS MET ASP ALA PHE GLU SEQRES 21 A 356 ARG SER PHE CYS ILE PHE ARG LEU PRO GLN PRO GLY SER SEQRES 22 A 356 TRP LYS ALA VAL ARG VAL ASP LEU VAL VAL ALA PRO VAL SEQRES 23 A 356 SER GLN PHE PRO PHE ALA LEU LEU GLY TRP THR GLY SER SEQRES 24 A 356 LYS LEU PHE GLN ARG GLU LEU ARG ARG PHE SER ARG LYS SEQRES 25 A 356 GLU LYS GLY LEU TRP LEU ASN SER HIS GLY LEU PHE ASP SEQRES 26 A 356 PRO GLU GLN LYS THR PHE PHE GLN ALA ALA SER GLU GLU SEQRES 27 A 356 ASP ILE PHE ARG HIS LEU GLY LEU GLU TYR LEU PRO PRO SEQRES 28 A 356 GLU GLN ARG ASN ALA SEQRES 1 T 9 DC DG DG DC DC DT DA DC DG SEQRES 1 P 5 DC DG DT DA DG SEQRES 1 D 4 DG DC DC DG HET MN A 501 1 HET MN A 502 1 HET MN A 503 1 HET MN A 504 1 HET MN A 505 1 HET NA A 506 1 HET PPV A 507 18 HET EDO A 508 4 HET EDO A 509 3 HET EDO A 510 4 HET EDO A 511 4 HET EDO A 512 4 HET EPE A 513 5 HET DTT A 514 1 HET MN T 101 1 HET MN P 101 1 HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM PPV PYROPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 5 MN 7(MN 2+) FORMUL 10 NA NA 1+ FORMUL 11 PPV H4 O7 P2 FORMUL 12 EDO 5(C2 H6 O2) FORMUL 17 EPE C8 H18 N2 O4 S FORMUL 18 DTT C4 H10 O2 S2 FORMUL 21 HOH *298(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 ARG A 230 1 9 HELIX 7 AA7 SER A 231 ILE A 243 1 13 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 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 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 SG CYS A 180 S1 DTT A 514 1555 1555 2.03 LINK ND1 HIS A 208 MN MN A 504 1555 1555 2.42 LINK OE1 GLU A 218 MN MN A 505 1555 1555 2.61 LINK NE2 HIS A 219 MN MN A 505 1555 1555 2.12 LINK O THR A 241 NA NA A 506 1555 1555 2.30 LINK O ILE A 243 NA NA A 506 1555 1555 2.40 LINK O VAL A 246 NA NA A 506 1555 1555 2.24 LINK OD2 ASP A 330 MN MN A 501 1555 1555 1.96 LINK OD1 ASP A 330 MN MN A 502 1555 1555 2.19 LINK OD1 ASP A 332 MN MN A 501 1555 1555 2.07 LINK OD2 ASP A 332 MN MN A 502 1555 1555 2.17 LINK OE1 GLU A 386 MN MN A 503 1555 1555 2.64 LINK OE2 GLU A 386 MN MN A 503 1555 1555 2.19 LINK OD2 ASP A 418 MN MN A 501 1555 1555 2.02 LINK NE2 HIS A 459 MN MN A 503 1555 1555 2.33 LINK MN MN A 501 O3' DA P 4 1555 1555 2.73 LINK MN MN A 501 OP1 DG P 5 1555 1555 2.16 LINK MN MN A 501 O HOH P 201 1555 1555 2.32 LINK MN MN A 502 O12BPPV A 507 1555 1555 2.10 LINK MN MN A 502 O32APPV A 507 1555 1555 2.33 LINK MN MN A 502 O11BPPV A 507 1555 1555 2.12 LINK MN MN A 502 O21APPV A 507 1555 1555 2.12 LINK MN MN A 502 O HOH A 699 1555 1555 2.10 LINK MN MN A 502 OP1 DG P 5 1555 1555 2.27 LINK MN MN A 503 O HOH A 774 1555 1555 2.31 LINK MN MN A 503 O HOH A 800 1555 1555 2.06 LINK MN MN A 503 O HOH T 203 1555 1555 2.30 LINK MN MN A 504 O HOH A 810 1555 1555 2.22 LINK MN MN A 504 OP3 DG D 1 1555 1555 2.24 LINK MN MN A 504 O HOH D 105 1555 1555 2.24 LINK MN MN A 505 O HOH A 602 1555 1555 2.03 LINK MN MN A 505 O HOH A 709 1555 1555 2.35 LINK MN MN A 505 O HOH A 735 1555 1555 1.93 LINK NA NA A 506 O HOH A 779 1555 1555 2.43 LINK NA NA A 506 OP1 DT P 3 1555 1555 2.65 LINK NA NA A 506 O HOH P 213 1555 1555 2.53 LINK O22APPV A 507 MN A MN P 101 1555 1555 2.11 LINK O AHOH A 778 MN A MN P 101 1555 1555 2.16 LINK N7 DG T 2 MN MN T 101 1555 1555 2.64 LINK MN MN T 101 O HOH T 201 1555 1555 2.48 LINK MN MN T 101 O HOH T 205 1555 1555 2.30 LINK MN MN T 101 O HOH T 224 1555 1555 2.21 LINK OP2 DG P 5 MN A MN P 101 1555 1555 2.20 LINK MN A MN P 101 O AHOH P 208 1555 1555 2.36 LINK MN A MN P 101 O AHOH P 212 1555 1555 1.79 CISPEP 1 GLY A 436 SER A 437 0 -6.10 CRYST1 59.985 68.882 109.747 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 0.016671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009112 0.00000