HEADER REPLICATION 03-JAN-20 6VF9 TITLE DNA POLYMERASE MU, 8-OXORGTP:CT TERNARY COMPLEX, 50 MM MG2+ (2160 MIN) 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*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 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: 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 TIME-LAPSE CRYSTALLOGRAPHY, OXIDIZED RIBONUCLEOTIDE INSERTION, DNA KEYWDS 2 POLYMERASE MU, DOUBLE STRAND BREAK REPAIR, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JAMSEN,S.H.WILSON REVDAT 3 06-NOV-24 6VF9 1 REMARK REVDAT 2 11-OCT-23 6VF9 1 REMARK REVDAT 1 01-SEP-21 6VF9 0 JRNL AUTH J.A.JAMSEN,A.SASSA,D.D.SHOCK,W.A.BEARD,S.H.WILSON JRNL TITL DNA POLYMERASE MU, 8-OXORGTP:CT TERNARY COMPLEX, 50 MM MG2+ JRNL TITL 2 (2160 MIN) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.56 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 63419 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 3155 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 34.9280 - 4.4329 0.96 2749 149 0.1812 0.2038 REMARK 3 2 4.4329 - 3.5196 0.99 2722 134 0.1473 0.1576 REMARK 3 3 3.5196 - 3.0750 1.00 2673 144 0.1589 0.1666 REMARK 3 4 3.0750 - 2.7940 1.00 2661 150 0.1728 0.1748 REMARK 3 5 2.7940 - 2.5938 0.99 2646 139 0.1617 0.1981 REMARK 3 6 2.5938 - 2.4409 0.97 2563 135 0.1547 0.1888 REMARK 3 7 2.4409 - 2.3187 0.99 2615 142 0.1493 0.1493 REMARK 3 8 2.3187 - 2.2178 0.99 2610 125 0.1484 0.1836 REMARK 3 9 2.2178 - 2.1324 1.00 2655 155 0.1564 0.1692 REMARK 3 10 2.1324 - 2.0588 0.99 2601 134 0.1677 0.1720 REMARK 3 11 2.0588 - 1.9945 0.99 2634 130 0.1654 0.1717 REMARK 3 12 1.9945 - 1.9375 1.00 2600 135 0.1614 0.2005 REMARK 3 13 1.9375 - 1.8865 0.99 2607 127 0.1672 0.2436 REMARK 3 14 1.8865 - 1.8404 0.99 2632 113 0.1702 0.1865 REMARK 3 15 1.8404 - 1.7986 0.96 2507 158 0.1701 0.1809 REMARK 3 16 1.7986 - 1.7603 0.99 2584 138 0.1690 0.2110 REMARK 3 17 1.7603 - 1.7251 0.99 2589 130 0.1719 0.1687 REMARK 3 18 1.7251 - 1.6926 1.00 2614 143 0.1725 0.1827 REMARK 3 19 1.6926 - 1.6623 1.00 2594 132 0.1825 0.2045 REMARK 3 20 1.6623 - 1.6342 1.00 2615 125 0.1977 0.1927 REMARK 3 21 1.6342 - 1.6078 1.00 2600 147 0.2018 0.2201 REMARK 3 22 1.6078 - 1.5831 1.00 2599 134 0.2273 0.2480 REMARK 3 23 1.5831 - 1.5600 0.98 2594 136 0.2405 0.2565 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) : 16.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 137 THROUGH 494) REMARK 3 ORIGIN FOR THE GROUP (A): 5.0467 -4.5641 -11.8392 REMARK 3 T TENSOR REMARK 3 T11: 0.1331 T22: 0.1524 REMARK 3 T33: 0.1306 T12: 0.0031 REMARK 3 T13: -0.0235 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.1023 L22: 1.0557 REMARK 3 L33: 1.0430 L12: -0.1285 REMARK 3 L13: -0.2806 L23: 0.3106 REMARK 3 S TENSOR REMARK 3 S11: 0.0196 S12: 0.0158 S13: -0.0422 REMARK 3 S21: 0.0570 S22: -0.0413 S23: -0.0488 REMARK 3 S31: -0.0446 S32: 0.0755 S33: -0.0024 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'T' AND RESID 1 THROUGH 9) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2643 -6.4321 -25.7362 REMARK 3 T TENSOR REMARK 3 T11: 0.2682 T22: 0.2048 REMARK 3 T33: 0.1672 T12: 0.0374 REMARK 3 T13: -0.0317 T23: -0.0384 REMARK 3 L TENSOR REMARK 3 L11: 0.1042 L22: 0.0946 REMARK 3 L33: 0.1788 L12: 0.0880 REMARK 3 L13: -0.0969 L23: -0.1243 REMARK 3 S TENSOR REMARK 3 S11: 0.1540 S12: 0.1203 S13: -0.0261 REMARK 3 S21: -0.5858 S22: -0.1568 S23: 0.1264 REMARK 3 S31: -0.2779 S32: -0.1686 S33: 0.0025 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'P' AND RESID 1 THROUGH 4) REMARK 3 ORIGIN FOR THE GROUP (A): 3.2821 4.1224 -18.8551 REMARK 3 T TENSOR REMARK 3 T11: 0.2396 T22: 0.2219 REMARK 3 T33: 0.1687 T12: -0.0180 REMARK 3 T13: -0.0244 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.0228 L22: 0.0136 REMARK 3 L33: 0.0111 L12: 0.0001 REMARK 3 L13: -0.0008 L23: 0.0123 REMARK 3 S TENSOR REMARK 3 S11: 0.1098 S12: 0.0185 S13: -0.1086 REMARK 3 S21: -0.0110 S22: -0.0887 S23: 0.0623 REMARK 3 S31: 0.0749 S32: 0.0349 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): 6.5602 -20.0615 -29.4646 REMARK 3 T TENSOR REMARK 3 T11: 0.2017 T22: 0.2323 REMARK 3 T33: 0.1800 T12: 0.0089 REMARK 3 T13: -0.0104 T23: -0.0528 REMARK 3 L TENSOR REMARK 3 L11: 0.4446 L22: 0.6111 REMARK 3 L33: 1.0274 L12: -0.5185 REMARK 3 L13: 0.6732 L23: -0.7925 REMARK 3 S TENSOR REMARK 3 S11: 0.0142 S12: -0.1129 S13: -0.1433 REMARK 3 S21: -0.1682 S22: 0.1972 S23: 0.0059 REMARK 3 S31: 0.2084 S32: -0.2323 S33: 0.0790 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 6VF9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000244074. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63490 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.91100 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 (%): 49.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 85-90MM HEPES PH 7.5, 17-18% PEG4000, 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 30.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.26650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.06500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.26650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.06500 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: 5650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 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 TRP A 137 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 137 CZ3 CH2 REMARK 470 LEU A 196 CD1 CD2 REMARK 470 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 207 OE1 OE2 REMARK 470 GLU A 218 CG CD OE1 OE2 REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 LYS A 249 CE NZ REMARK 470 GLU A 267 OE1 OE2 REMARK 470 GLN A 268 CG CD OE1 NE2 REMARK 470 GLN A 270 CB CG CD OE1 NE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 274 CG CD OE1 NE2 REMARK 470 GLN A 284 CD OE1 NE2 REMARK 470 GLN A 300 CD OE1 NE2 REMARK 470 GLU A 304 CD OE1 OE2 REMARK 470 LYS A 339 CE NZ REMARK 470 GLN A 355 CD OE1 NE2 REMARK 470 GLN A 364 OE1 NE2 REMARK 470 LYS A 438 NZ REMARK 470 LYS A 467 CD CE NZ REMARK 470 GLU A 485 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' -0.048 REMARK 500 DT P 3 O3' DT P 3 C3' -0.043 REMARK 500 DG D 1 P DG D 1 OP3 -0.123 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 ASP A 285 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.2 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 SER A 172 79.20 -100.15 REMARK 500 LEU A 310 104.90 -160.06 REMARK 500 THR A 318 -149.16 -122.38 REMARK 500 THR A 318 -159.80 -130.09 REMARK 500 SER A 411 -149.17 -165.02 REMARK 500 ASN A 493 49.35 -86.84 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 504 REMARK 610 EPE A 509 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 506 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 97.7 REMARK 620 3 VAL A 246 O 89.9 92.2 REMARK 620 4 HOH A 825 O 88.7 91.4 176.3 REMARK 620 5 DT P 3 OP1 170.6 91.3 92.3 88.5 REMARK 620 6 HOH P 112 O 90.8 170.8 84.2 92.4 80.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 505 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 138.3 REMARK 620 3 ASP A 332 OD2 108.5 48.2 REMARK 620 4 ASP A 418 OD2 114.5 82.5 130.2 REMARK 620 5 HOH P 101 O 78.2 114.4 72.1 139.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 507 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 117.0 REMARK 620 3 HOH A 628 O 85.4 111.6 REMARK 620 4 HOH A 708 O 133.8 108.1 87.0 REMARK 620 5 HOH P 101 O 85.5 71.4 170.7 100.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 DTT A 510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VEZ RELATED DB: PDB DBREF 6VF9 A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 6VF9 T 1 9 PDB 6VF9 6VF9 1 9 DBREF 6VF9 P 1 4 PDB 6VF9 6VF9 1 4 DBREF 6VF9 D 1 4 PDB 6VF9 6VF9 1 4 SEQADV 6VF9 GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF9 SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF9 ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF9 ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF9 ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF9 A UNP Q9NP87 PRO 398 DELETION SEQADV 6VF9 A UNP Q9NP87 GLY 399 DELETION SEQADV 6VF9 A UNP Q9NP87 ALA 400 DELETION SEQADV 6VF9 A UNP Q9NP87 ALA 401 DELETION SEQADV 6VF9 A UNP Q9NP87 VAL 402 DELETION SEQADV 6VF9 A UNP Q9NP87 GLY 403 DELETION SEQADV 6VF9 A UNP Q9NP87 GLY 404 DELETION SEQADV 6VF9 A UNP Q9NP87 SER 405 DELETION SEQADV 6VF9 A UNP Q9NP87 THR 406 DELETION SEQADV 6VF9 A UNP Q9NP87 ARG 407 DELETION SEQADV 6VF9 A UNP Q9NP87 PRO 408 DELETION SEQADV 6VF9 A UNP Q9NP87 CYS 409 DELETION SEQADV 6VF9 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 4 DC DG DT DA SEQRES 1 D 4 DG DC DC DG HET EDO A 501 4 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 3 HET MG A 505 1 HET NA A 506 1 HET NA A 507 1 HET CL A 508 1 HET EPE A 509 5 HET DTT A 510 2 HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION 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 EDO 4(C2 H6 O2) FORMUL 9 MG MG 2+ FORMUL 10 NA 2(NA 1+) FORMUL 12 CL CL 1- FORMUL 13 EPE C8 H18 N2 O4 S FORMUL 14 DTT C4 H10 O2 S2 FORMUL 15 HOH *352(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 VAL A 331 THR A 336 -1 O LEU A 334 N THR A 316 SHEET 3 AA2 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335 SHEET 4 AA2 5 ARG A 387 GLN A 396 -1 N PHE A 392 O VAL A 415 SHEET 5 AA2 5 ILE A 360 TYR A 362 -1 N LEU A 361 O ILE A 391 SHEET 1 AA3 3 TRP A 455 ASN A 457 0 SHEET 2 AA3 3 GLY A 460 ASP A 463 -1 O PHE A 462 N TRP A 455 SHEET 3 AA3 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463 LINK SG ACYS A 180 S1 ADTT A 510 1555 1555 1.95 LINK SG BCYS A 180 S1 BDTT A 510 1555 1555 2.04 LINK O THR A 241 NA NA A 506 1555 1555 2.42 LINK O ILE A 243 NA NA A 506 1555 1555 2.44 LINK O VAL A 246 NA NA A 506 1555 1555 2.30 LINK OD2 ASP A 330 MG MG A 505 1555 1555 2.07 LINK OD1 ASP A 330 NA NA A 507 1555 1555 2.14 LINK OD1 ASP A 332 MG MG A 505 1555 1555 1.98 LINK OD2 ASP A 332 MG MG A 505 1555 1555 2.90 LINK OD2 ASP A 332 NA NA A 507 1555 1555 2.31 LINK OD2 ASP A 418 MG MG A 505 1555 1555 1.94 LINK MG MG A 505 O HOH P 101 1555 1555 1.91 LINK NA NA A 506 O HOH A 825 1555 1555 2.29 LINK NA NA A 506 OP1 DT P 3 1555 1555 2.75 LINK NA NA A 506 O HOH P 112 1555 1555 2.40 LINK NA NA A 507 O HOH A 628 1555 1555 2.46 LINK NA NA A 507 O HOH A 708 1555 1555 2.02 LINK NA NA A 507 O HOH P 101 1555 1555 2.71 CISPEP 1 GLY A 436 SER A 437 0 -5.82 SITE 1 AC1 8 GLY A 433 TRP A 434 GLN A 441 ARG A 445 SITE 2 AC1 8 SER A 458 EDO A 504 HOH A 797 DA P 4 SITE 1 AC2 6 HIS A 152 THR A 314 THR A 336 PHE A 427 SITE 2 AC2 6 HOH A 611 HOH A 630 SITE 1 AC3 5 HIS A 204 ARG A 446 DC D 3 HOH D 114 SITE 2 AC3 5 HOH D 116 SITE 1 AC4 6 ARG A 387 ARG A 445 SER A 458 EDO A 501 SITE 2 AC4 6 DT T 6 DA T 7 SITE 1 AC5 6 ASP A 330 ASP A 332 ASP A 418 NA A 507 SITE 2 AC5 6 DA P 4 HOH P 101 SITE 1 AC6 6 THR A 241 ILE A 243 VAL A 246 HOH A 825 SITE 2 AC6 6 DT P 3 HOH P 112 SITE 1 AC7 6 ASP A 330 ASP A 332 MG A 505 HOH A 628 SITE 2 AC7 6 HOH A 708 HOH P 101 SITE 1 AC8 4 SER A 172 GLY A 174 ARG A 175 HOH A 761 SITE 1 AC9 4 LEU A 149 LYS A 325 LEU A 326 GLN A 327 SITE 1 AD1 1 CYS A 180 CRYST1 60.200 62.130 118.533 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 0.016611 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016095 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008436 0.00000