HEADER REPLICATION 03-JAN-20 6VF0 TITLE DNA POLYMERASE MU, 8-OXORGTP:AT REACTION STATE TERNARY COMPLEX, 50 MM TITLE 2 MG2+ (30 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*AP*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*(8GM))-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 4 03-SEP-25 6VF0 1 JRNL REVDAT 3 30-OCT-24 6VF0 1 REMARK REVDAT 2 11-OCT-23 6VF0 1 REMARK REVDAT 1 01-SEP-21 6VF0 0 JRNL AUTH J.A.JAMSEN,A.SASSA,L.PERERA,D.D.SHOCK,W.A.BEARD,S.H.WILSON JRNL TITL STRUCTURAL BASIS FOR PROFICIENT OXIDIZED RIBONUCLEOTIDE JRNL TITL 2 INSERTION IN DOUBLE STRAND BREAK REPAIR. JRNL REF NAT COMMUN V. 12 5055 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34417448 JRNL DOI 10.1038/S41467-021-24486-X REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 63471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3176 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 34.9560 - 4.4734 0.99 2829 148 0.1778 0.2060 REMARK 3 2 4.4734 - 3.5518 1.00 2696 142 0.1397 0.1547 REMARK 3 3 3.5518 - 3.1031 1.00 2676 141 0.1549 0.1646 REMARK 3 4 3.1031 - 2.8195 1.00 2664 142 0.1669 0.1930 REMARK 3 5 2.8195 - 2.6175 1.00 2651 139 0.1639 0.1814 REMARK 3 6 2.6175 - 2.4632 1.00 2644 139 0.1535 0.1800 REMARK 3 7 2.4632 - 2.3399 1.00 2627 139 0.1470 0.1775 REMARK 3 8 2.3399 - 2.2381 1.00 2628 137 0.1485 0.1865 REMARK 3 9 2.2381 - 2.1519 1.00 2631 139 0.1532 0.1883 REMARK 3 10 2.1519 - 2.0777 1.00 2622 140 0.1620 0.1952 REMARK 3 11 2.0777 - 2.0127 1.00 2619 137 0.1599 0.1974 REMARK 3 12 2.0127 - 1.9552 1.00 2628 137 0.1713 0.1841 REMARK 3 13 1.9552 - 1.9037 1.00 2617 136 0.1685 0.1823 REMARK 3 14 1.9037 - 1.8573 1.00 2598 139 0.1665 0.2032 REMARK 3 15 1.8573 - 1.8151 1.00 2621 138 0.1706 0.1816 REMARK 3 16 1.8151 - 1.7764 1.00 2614 137 0.1758 0.2001 REMARK 3 17 1.7764 - 1.7409 1.00 2621 139 0.1897 0.1988 REMARK 3 18 1.7409 - 1.7081 1.00 2575 136 0.1963 0.2160 REMARK 3 19 1.7081 - 1.6775 1.00 2595 136 0.2016 0.2795 REMARK 3 20 1.6775 - 1.6491 1.00 2594 138 0.2125 0.2379 REMARK 3 21 1.6491 - 1.6225 1.00 2599 134 0.2159 0.2344 REMARK 3 22 1.6225 - 1.5975 1.00 2603 138 0.2300 0.2529 REMARK 3 23 1.5975 - 1.5800 0.91 2343 125 0.2571 0.2756 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.90 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 2.9063 -4.2900 -11.6085 REMARK 3 T TENSOR REMARK 3 T11: 0.1933 T22: 0.1983 REMARK 3 T33: 0.1617 T12: 0.0064 REMARK 3 T13: -0.0034 T23: 0.0113 REMARK 3 L TENSOR REMARK 3 L11: 1.1711 L22: 0.9508 REMARK 3 L33: 0.7216 L12: -0.2447 REMARK 3 L13: -0.1772 L23: 0.1498 REMARK 3 S TENSOR REMARK 3 S11: 0.0547 S12: 0.1229 S13: 0.0613 REMARK 3 S21: -0.0516 S22: -0.0337 S23: -0.0519 REMARK 3 S31: 0.0087 S32: 0.0257 S33: 0.0001 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 6VF0 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_1000244086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-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 : 63540 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.574 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.97100 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 (%): 50.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 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 29.99100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.30750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.21850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.30750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.99100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.21850 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: 7070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 CG CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 GLU A 223 OE1 OE2 REMARK 470 LYS A 249 NZ REMARK 470 GLU A 267 CG CD OE1 OE2 REMARK 470 GLN A 268 CG CD OE1 NE2 REMARK 470 GLN A 270 CG CD OE1 NE2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 274 CG CD OE1 NE2 REMARK 470 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 HIS A 363 ND1 CD2 CE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 LYS A 413 NZ REMARK 470 GLU A 465 CG CD OE1 OE2 REMARK 470 GLN A 466 OE1 NE2 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' -0.046 REMARK 500 DG D 1 P DG D 1 OP3 -0.106 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. = 2.9 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC T 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG T 9 O4' - C1' - N9 ANGL. DEV. = -4.7 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 38.68 -140.34 REMARK 500 SER A 172 79.19 -100.15 REMARK 500 LEU A 310 95.21 -160.77 REMARK 500 THR A 318 -150.08 -121.55 REMARK 500 THR A 318 -156.92 -127.89 REMARK 500 PRO A 397 107.62 -45.90 REMARK 500 SER A 411 -145.45 -168.17 REMARK 500 ASN A 493 49.16 -87.88 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 902 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 903 DISTANCE = 6.08 ANGSTROMS 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 508 REMARK 610 EDO A 509 REMARK 610 EDO A 510 REMARK 610 EPE A 511 REMARK 610 PPV P 102 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 96.8 REMARK 620 3 VAL A 246 O 89.6 91.6 REMARK 620 4 HOH A 824 O 85.2 88.3 174.7 REMARK 620 5 DT P 3 OP1 171.9 91.1 91.8 93.5 REMARK 620 6 HOH P 216 O 88.8 174.4 87.5 93.1 83.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 281 OE1 REMARK 620 2 HOH A 689 O 126.8 REMARK 620 3 HOH A 833 O 93.1 112.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 103.0 REMARK 620 3 ASP A 418 OD2 100.2 89.8 REMARK 620 4 8GT A 505 O2A 96.4 93.5 161.9 REMARK 620 5 HOH A 605 O 73.8 175.2 94.2 83.4 REMARK 620 6 DA P 4 O3' 156.9 97.9 89.4 72.5 84.7 REMARK 620 7 DA P 4 O3' 155.2 99.7 89.4 72.5 82.9 1.9 REMARK 620 8 8GM P 5 OP1 105.3 93.0 153.0 9.1 84.5 63.6 63.6 REMARK 620 N 1 2 3 4 5 6 7 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 100.7 REMARK 620 3 8GT A 505 O2A 96.1 89.1 REMARK 620 4 8GT A 505 O1G 78.2 178.3 92.3 REMARK 620 5 8GT A 505 O2B 165.3 93.7 86.5 87.3 REMARK 620 6 HOH A 661 O 87.9 88.4 175.6 90.3 90.0 REMARK 620 7 8GM P 5 OP1 89.5 78.9 13.4 102.3 95.8 166.3 REMARK 620 8 PPV P 102 O21 159.5 99.2 88.9 81.8 5.9 87.9 99.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VEZ RELATED DB: PDB DBREF 6VF0 A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 6VF0 T 1 9 PDB 6VF0 6VF0 1 9 DBREF 6VF0 P 1 5 PDB 6VF0 6VF0 1 5 DBREF 6VF0 D 1 4 PDB 6VF0 6VF0 1 4 SEQADV 6VF0 GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF0 SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF0 ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF0 ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF0 ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 6VF0 A UNP Q9NP87 PRO 398 DELETION SEQADV 6VF0 A UNP Q9NP87 GLY 399 DELETION SEQADV 6VF0 A UNP Q9NP87 ALA 400 DELETION SEQADV 6VF0 A UNP Q9NP87 ALA 401 DELETION SEQADV 6VF0 A UNP Q9NP87 VAL 402 DELETION SEQADV 6VF0 A UNP Q9NP87 GLY 403 DELETION SEQADV 6VF0 A UNP Q9NP87 GLY 404 DELETION SEQADV 6VF0 A UNP Q9NP87 SER 405 DELETION SEQADV 6VF0 A UNP Q9NP87 THR 406 DELETION SEQADV 6VF0 A UNP Q9NP87 ARG 407 DELETION SEQADV 6VF0 A UNP Q9NP87 PRO 408 DELETION SEQADV 6VF0 A UNP Q9NP87 CYS 409 DELETION SEQADV 6VF0 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 DA DT DA DC DG SEQRES 1 P 5 DC DG DT DA 8GM SEQRES 1 D 4 DG DC DC DG HET 8GM P 5 24 HET MG A 501 1 HET MG A 502 1 HET NA A 503 1 HET NA A 504 1 HET 8GT A 505 33 HET DTT A 506 1 HET EDO A 507 4 HET EDO A 508 3 HET EDO A 509 3 HET EDO A 510 3 HET EPE A 511 4 HET CL A 512 1 HET EDO P 101 4 HET PPV P 102 5 HETNAM 8GM [(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7- HETNAM 2 8GM DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 3 8GM DIHYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM 8GT 8-OXO-GUANOSINE-5'-TRIPHOSPHATE HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM CL CHLORIDE ION HETNAM PPV PYROPHOSPHATE HETSYN 8GM 8-OXOGUANOSINE-5'-PHOSPHATE HETSYN DTT 1,4-DITHIOTHREITOL HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 3 8GM C10 H14 N5 O9 P FORMUL 5 MG 2(MG 2+) FORMUL 7 NA 2(NA 1+) FORMUL 9 8GT C10 H16 N5 O15 P3 FORMUL 10 DTT C4 H10 O2 S2 FORMUL 11 EDO 5(C2 H6 O2) FORMUL 15 EPE C8 H18 N2 O4 S FORMUL 16 CL CL 1- FORMUL 18 PPV H4 O7 P2 FORMUL 19 HOH *378(H2 O) HELIX 1 AA1 TYR A 141 ARG A 145 5 5 HELIX 2 AA2 ASN A 153 GLU A 170 1 18 HELIX 3 AA3 SER A 172 LEU A 189 1 18 HELIX 4 AA4 THR A 195 GLN A 200 5 6 HELIX 5 AA5 GLY A 206 GLY A 220 1 15 HELIX 6 AA6 CYS A 222 SER A 231 1 10 HELIX 7 AA7 SER A 231 GLN A 242 1 12 HELIX 8 AA8 GLY A 247 GLU A 257 1 11 HELIX 9 AA9 THR A 261 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 SG ACYS A 180 S1 ADTT A 506 1555 1555 2.01 LINK O3'B DA P 4 P B8GM P 5 1555 1555 1.61 LINK O THR A 241 NA NA A 503 1555 1555 2.43 LINK O ILE A 243 NA NA A 503 1555 1555 2.40 LINK O VAL A 246 NA NA A 503 1555 1555 2.35 LINK OE1 GLN A 281 NA NA A 504 1555 1555 2.27 LINK OD2 ASP A 330 MG MG A 501 1555 1555 1.77 LINK OD1 ASP A 330 MG MG A 502 1555 1555 2.01 LINK OD1 ASP A 332 MG MG A 501 1555 1555 2.15 LINK OD2 ASP A 332 MG MG A 502 1555 1555 2.15 LINK OD2 ASP A 418 MG MG A 501 1555 1555 2.07 LINK MG MG A 501 O2AA8GT A 505 1555 1555 2.46 LINK MG MG A 501 O HOH A 605 1555 1555 2.19 LINK MG MG A 501 O3'A DA P 4 1555 1555 2.89 LINK MG MG A 501 O3'B DA P 4 1555 1555 2.73 LINK MG MG A 501 OP1B8GM P 5 1555 1555 1.88 LINK MG MG A 502 O2AA8GT A 505 1555 1555 1.98 LINK MG MG A 502 O1GA8GT A 505 1555 1555 2.31 LINK MG MG A 502 O2BA8GT A 505 1555 1555 2.15 LINK MG MG A 502 O HOH A 661 1555 1555 2.07 LINK MG MG A 502 OP1B8GM P 5 1555 1555 2.43 LINK MG MG A 502 O21BPPV P 102 1555 1555 2.05 LINK NA NA A 503 O HOH A 824 1555 1555 2.31 LINK NA NA A 503 OP1 DT P 3 1555 1555 2.65 LINK NA NA A 503 O HOH P 216 1555 1555 2.37 LINK NA NA A 504 O HOH A 689 1555 1555 2.63 LINK NA NA A 504 O HOH A 833 1555 1555 2.27 CISPEP 1 GLY A 436 SER A 437 0 -9.01 CRYST1 59.982 68.437 110.615 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 0.016672 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014612 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009040 0.00000 CONECT 368 3186 CONECT 847 3151 CONECT 863 3151 CONECT 886 3151 CONECT 1168 3152 CONECT 1570 3150 CONECT 1571 3149 CONECT 1585 3149 CONECT 1586 3150 CONECT 2055 3149 CONECT 2938 3151 CONECT 2973 3149 CONECT 2974 2999 3149 CONECT 2999 2974 3000 3001 3002 CONECT 3000 2999 CONECT 3001 2999 3149 3150 CONECT 3002 2999 3003 CONECT 3003 3002 3004 CONECT 3004 3003 3005 3006 CONECT 3005 3004 3010 CONECT 3006 3004 3007 3008 CONECT 3007 3006 CONECT 3008 3006 3009 3010 CONECT 3009 3008 CONECT 3010 3005 3008 3011 CONECT 3011 3010 3012 3014 CONECT 3012 3011 3013 3022 CONECT 3013 3012 CONECT 3014 3011 3015 3021 CONECT 3015 3014 3016 CONECT 3016 3015 3017 3018 CONECT 3017 3016 CONECT 3018 3016 3019 CONECT 3019 3018 3020 3021 CONECT 3020 3019 CONECT 3021 3014 3019 3022 CONECT 3022 3012 3021 CONECT 3149 1571 1585 2055 2973 CONECT 3149 2974 3001 3164 3218 CONECT 3150 1570 1586 3001 3154 CONECT 3150 3160 3164 3211 3275 CONECT 3151 847 863 886 2938 CONECT 3151 3441 3582 CONECT 3152 1168 3303 3452 CONECT 3153 3154 3155 3156 3157 CONECT 3154 3150 3153 CONECT 3155 3153 CONECT 3156 3153 CONECT 3157 3153 3158 CONECT 3158 3157 3159 3160 3161 CONECT 3159 3158 CONECT 3160 3150 3158 CONECT 3161 3158 3162 CONECT 3162 3161 3163 3164 3165 CONECT 3163 3162 CONECT 3164 3149 3150 3162 CONECT 3165 3162 3166 CONECT 3166 3165 3167 CONECT 3167 3166 3168 3169 CONECT 3168 3167 3173 CONECT 3169 3167 3170 3171 CONECT 3170 3169 CONECT 3171 3169 3172 3173 CONECT 3172 3171 CONECT 3173 3168 3171 3174 CONECT 3174 3173 3175 3184 CONECT 3175 3174 3176 3185 CONECT 3176 3175 3177 CONECT 3177 3176 3178 3184 CONECT 3178 3177 3179 3180 CONECT 3179 3178 CONECT 3180 3178 3181 CONECT 3181 3180 3182 3183 CONECT 3182 3181 CONECT 3183 3181 3184 CONECT 3184 3174 3177 3183 CONECT 3185 3175 CONECT 3186 368 CONECT 3187 3188 3189 CONECT 3188 3187 CONECT 3189 3187 3190 CONECT 3190 3189 CONECT 3191 3192 3193 CONECT 3192 3191 CONECT 3193 3191 CONECT 3194 3195 3196 CONECT 3195 3194 CONECT 3196 3194 CONECT 3197 3198 3199 CONECT 3198 3197 CONECT 3199 3197 CONECT 3200 3201 3202 3203 CONECT 3201 3200 CONECT 3202 3200 CONECT 3203 3200 CONECT 3205 3206 3207 CONECT 3206 3205 CONECT 3207 3205 3208 CONECT 3208 3207 CONECT 3209 3210 CONECT 3210 3209 3211 3212 3213 CONECT 3211 3150 3210 CONECT 3212 3210 CONECT 3213 3210 CONECT 3218 3149 CONECT 3275 3150 CONECT 3303 3152 CONECT 3441 3151 CONECT 3452 3152 CONECT 3582 3151 MASTER 441 0 15 20 10 0 0 6 3342 4 110 31 END