HEADER REPLICATION/DNA 24-NOV-20 7KT2 TITLE DNA POLYMERASE MU, DGTP:AT PRODUCT STATE TERNARY COMPLEX, 50 MM MN2+ TITLE 2 (225MIN) 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*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 7KT2 1 REMARK REVDAT 1 19-JAN-22 7KT2 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 73590 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3677 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 34.9580 - 4.4382 1.00 2914 154 0.1827 0.2067 REMARK 3 2 4.4382 - 3.5238 1.00 2768 147 0.1499 0.1523 REMARK 3 3 3.5238 - 3.0787 1.00 2767 145 0.1610 0.1832 REMARK 3 4 3.0787 - 2.7973 1.00 2725 144 0.1681 0.1734 REMARK 3 5 2.7973 - 2.5969 1.00 2704 143 0.1656 0.1943 REMARK 3 6 2.5969 - 2.4438 1.00 2744 142 0.1582 0.1804 REMARK 3 7 2.4438 - 2.3215 1.00 2686 142 0.1535 0.1804 REMARK 3 8 2.3215 - 2.2204 1.00 2697 142 0.1524 0.1724 REMARK 3 9 2.2204 - 2.1350 1.00 2685 143 0.1581 0.2008 REMARK 3 10 2.1350 - 2.0613 1.00 2708 142 0.1612 0.1882 REMARK 3 11 2.0613 - 1.9969 1.00 2693 143 0.1614 0.2079 REMARK 3 12 1.9969 - 1.9398 1.00 2662 138 0.1673 0.1721 REMARK 3 13 1.9398 - 1.8887 1.00 2710 144 0.1704 0.2091 REMARK 3 14 1.8887 - 1.8426 1.00 2683 141 0.1610 0.1988 REMARK 3 15 1.8426 - 1.8008 1.00 2674 141 0.1642 0.1725 REMARK 3 16 1.8008 - 1.7624 1.00 2657 140 0.1706 0.2129 REMARK 3 17 1.7624 - 1.7272 1.00 2674 141 0.1712 0.1969 REMARK 3 18 1.7272 - 1.6946 1.00 2681 141 0.1786 0.2031 REMARK 3 19 1.6946 - 1.6643 1.00 2648 139 0.1907 0.2225 REMARK 3 20 1.6643 - 1.6361 1.00 2681 142 0.1925 0.2267 REMARK 3 21 1.6361 - 1.6097 1.00 2672 140 0.2072 0.2225 REMARK 3 22 1.6097 - 1.5850 1.00 2666 141 0.2118 0.2320 REMARK 3 23 1.5850 - 1.5617 1.00 2670 141 0.2177 0.2375 REMARK 3 24 1.5617 - 1.5397 0.99 2628 139 0.2283 0.2824 REMARK 3 25 1.5397 - 1.5188 0.98 2617 136 0.2499 0.2645 REMARK 3 26 1.5188 - 1.4991 0.94 2499 126 0.2597 0.2826 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.23 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 : 0.010 3193 REMARK 3 ANGLE : 1.107 4425 REMARK 3 CHIRALITY : 0.078 482 REMARK 3 PLANARITY : 0.008 504 REMARK 3 DIHEDRAL : 17.455 1196 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): 3.3930 -3.3538 -9.8986 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.1399 REMARK 3 T33: 0.1046 T12: 0.0045 REMARK 3 T13: 0.0151 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 1.7463 L22: 1.0010 REMARK 3 L33: 0.7475 L12: -0.4483 REMARK 3 L13: -0.1727 L23: 0.2088 REMARK 3 S TENSOR REMARK 3 S11: 0.1172 S12: 0.1238 S13: 0.1545 REMARK 3 S21: -0.0489 S22: -0.0694 S23: -0.1073 REMARK 3 S31: -0.0126 S32: 0.0306 S33: 0.0128 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'T' AND RESID 1 THROUGH 9) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9866 -6.2709 -24.2768 REMARK 3 T TENSOR REMARK 3 T11: 0.3074 T22: 0.3637 REMARK 3 T33: 0.1406 T12: 0.0538 REMARK 3 T13: -0.0263 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.3135 L22: 0.0626 REMARK 3 L33: 0.1553 L12: 0.1366 REMARK 3 L13: -0.2236 L23: -0.0942 REMARK 3 S TENSOR REMARK 3 S11: 0.1928 S12: 0.4262 S13: -0.0136 REMARK 3 S21: -0.4740 S22: -0.1835 S23: 0.0114 REMARK 3 S31: -0.1217 S32: -0.1363 S33: 0.0022 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'P' AND RESID 1 THROUGH 5) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4789 3.5633 -16.5502 REMARK 3 T TENSOR REMARK 3 T11: 0.2778 T22: 0.3124 REMARK 3 T33: 0.2765 T12: 0.0164 REMARK 3 T13: 0.0282 T23: 0.0866 REMARK 3 L TENSOR REMARK 3 L11: 0.0081 L22: 0.0081 REMARK 3 L33: 0.0222 L12: 0.0165 REMARK 3 L13: 0.0117 L23: 0.0100 REMARK 3 S TENSOR REMARK 3 S11: 0.2630 S12: -0.0394 S13: 0.0587 REMARK 3 S21: -0.0380 S22: -0.1049 S23: 0.1718 REMARK 3 S31: 0.2082 S32: -0.0374 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): 3.2901 -22.0235 -25.8504 REMARK 3 T TENSOR REMARK 3 T11: 0.3358 T22: 0.3892 REMARK 3 T33: 0.1686 T12: 0.0194 REMARK 3 T13: -0.0393 T23: -0.1335 REMARK 3 L TENSOR REMARK 3 L11: 0.0748 L22: 0.6072 REMARK 3 L33: 0.3443 L12: -0.1167 REMARK 3 L13: 0.0345 L23: -0.4230 REMARK 3 S TENSOR REMARK 3 S11: 0.0232 S12: 0.1423 S13: -0.1057 REMARK 3 S21: -0.3495 S22: -0.0359 S23: 0.1835 REMARK 3 S31: 0.3686 S32: -0.3976 S33: 0.3509 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 7KT2 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_1000253002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-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-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 : 73665 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.499 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.80500 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 (%): 50.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 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 29.94650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.15950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.43300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.15950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.94650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.43300 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: 7170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 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 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 ARG A 211 CZ NH1 NH2 REMARK 470 GLN A 214 CD OE1 NE2 REMARK 470 GLU A 218 OE1 OE2 REMARK 470 GLU A 223 CD OE1 OE2 REMARK 470 GLN A 235 CD OE1 NE2 REMARK 470 GLU A 267 CG CD OE1 OE2 REMARK 470 GLN A 268 CB CG CD OE1 NE2 REMARK 470 GLN A 270 CB CG CD OE1 NE2 REMARK 470 LYS A 271 CB CG CD CE NZ REMARK 470 GLN A 274 CG CD OE1 NE2 REMARK 470 ASP A 296 OD1 OD2 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 OE1 NE2 REMARK 470 GLN A 357 OE1 NE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 465 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' -0.038 REMARK 500 DT T 6 P DT T 6 O5' -0.068 REMARK 500 DT P 3 O3' DT P 3 C3' -0.083 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 ARG A 322 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 DC T 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 4.8 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 38.74 -141.71 REMARK 500 GLN A 268 60.30 -150.99 REMARK 500 THR A 318 -153.98 -123.37 REMARK 500 THR A 318 -157.49 -129.89 REMARK 500 PRO A 397 109.52 -47.36 REMARK 500 SER A 411 -143.28 -166.62 REMARK 500 ASN A 493 48.71 -86.44 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 EPE A 507 REMARK 610 EDO A 509 REMARK 610 EDO A 510 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 DG D 1 OP3 75.3 REMARK 620 3 HOH D 208 O 84.1 86.9 REMARK 620 4 HOH D 219 O 100.8 105.6 167.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 93.6 REMARK 620 3 VAL A 246 O 90.9 89.9 REMARK 620 4 HOH A 819 O 90.4 90.5 178.6 REMARK 620 5 DT P 3 OP1 175.9 90.4 88.1 90.6 REMARK 620 6 HOH P 216 O 90.0 176.4 89.6 89.9 86.0 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 98.3 REMARK 620 3 DGT A 511 O2B 84.7 169.7 REMARK 620 4 DGT A 511 O1G 163.0 94.4 84.7 REMARK 620 5 HOH A 735 O 82.8 84.5 105.6 87.2 REMARK 620 6 DG P 5 OP1 91.9 89.0 81.1 99.6 170.9 REMARK 620 N 1 2 3 4 5 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 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 96.6 REMARK 620 3 ASP A 418 OD2 99.4 96.9 REMARK 620 4 DA P 4 O3' 160.0 101.5 87.0 REMARK 620 5 DG P 5 OP1 107.4 91.9 150.5 63.6 REMARK 620 6 HOH P 202 O 77.7 172.8 88.4 83.6 85.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 506 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 386 OE1 REMARK 620 2 GLU A 386 OE2 56.6 REMARK 620 3 HOH A 817 O 91.7 99.7 REMARK 620 4 HOH A 841 O 118.7 172.7 85.6 REMARK 620 5 HOH T 103 O 97.1 94.0 166.2 80.8 REMARK 620 N 1 2 3 4 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 DGT A 511 O1B REMARK 620 2 HOH A 717 O 91.9 REMARK 620 3 DG P 5 OP2 90.9 176.4 REMARK 620 4 HOH P 210 O 175.6 85.1 92.0 REMARK 620 5 HOH P 212 O 97.6 86.6 95.3 85.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 1 N7 REMARK 620 2 HOH D 211 O 92.2 REMARK 620 3 HOH D 214 O 99.7 167.4 REMARK 620 N 1 2 DBREF 7KT2 A 127 494 UNP Q9NP87 DPOLM_HUMAN 127 494 DBREF 7KT2 T 1 9 PDB 7KT2 7KT2 1 9 DBREF 7KT2 P 1 5 PDB 7KT2 7KT2 1 5 DBREF 7KT2 D 1 4 PDB 7KT2 7KT2 1 4 SEQADV 7KT2 SER A 128 UNP Q9NP87 PRO 128 CONFLICT SEQADV 7KT2 ALA A 129 UNP Q9NP87 ARG 129 CONFLICT SEQADV 7KT2 ALA A 130 UNP Q9NP87 LYS 130 CONFLICT SEQADV 7KT2 ALA A 131 UNP Q9NP87 GLY 131 CONFLICT SEQADV 7KT2 A UNP Q9NP87 PRO 398 DELETION SEQADV 7KT2 A UNP Q9NP87 GLY 399 DELETION SEQADV 7KT2 A UNP Q9NP87 ALA 400 DELETION SEQADV 7KT2 A UNP Q9NP87 ALA 401 DELETION SEQADV 7KT2 A UNP Q9NP87 VAL 402 DELETION SEQADV 7KT2 A UNP Q9NP87 GLY 403 DELETION SEQADV 7KT2 A UNP Q9NP87 GLY 404 DELETION SEQADV 7KT2 A UNP Q9NP87 SER 405 DELETION SEQADV 7KT2 A UNP Q9NP87 THR 406 DELETION SEQADV 7KT2 A UNP Q9NP87 ARG 407 DELETION SEQADV 7KT2 A UNP Q9NP87 PRO 408 DELETION SEQADV 7KT2 A UNP Q9NP87 CYS 409 DELETION SEQADV 7KT2 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 DG SEQRES 1 D 4 DG DC DC DG HET NA A 501 1 HET MN A 502 1 HET MN A 503 1 HET MN A 504 1 HET MN A 505 1 HET MN A 506 1 HET EPE A 507 4 HET EDO A 508 4 HET EDO A 509 3 HET EDO A 510 2 HET DGT A 511 31 HET DTT A 512 1 HET MN P 101 1 HET EDO P 102 4 HET MN D 101 1 HETNAM NA SODIUM ION HETNAM MN MANGANESE (II) ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 5 NA NA 1+ FORMUL 6 MN 7(MN 2+) FORMUL 11 EPE C8 H18 N2 O4 S FORMUL 12 EDO 4(C2 H6 O2) FORMUL 15 DGT C10 H16 N5 O13 P3 FORMUL 16 DTT C4 H10 O2 S2 FORMUL 20 HOH *340(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 TYR A 362 O ILE A 391 SHEET 1 AA3 3 TRP A 455 LEU A 456 0 SHEET 2 AA3 3 LEU A 461 ASP A 463 -1 O PHE A 462 N TRP A 455 SHEET 3 AA3 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463 LINK SG CYS A 180 S1 DTT A 512 1555 1555 2.03 LINK ND1 HIS A 208 MN MN A 504 1555 1555 2.36 LINK NE2 HIS A 219 MN MN A 505 1555 1555 2.15 LINK O THR A 241 NA NA A 501 1555 1555 2.27 LINK O ILE A 243 NA NA A 501 1555 1555 2.38 LINK O VAL A 246 NA NA A 501 1555 1555 2.27 LINK OD1 ASP A 330 MN MN A 502 1555 1555 2.12 LINK OD2 ASP A 330 MN MN A 503 1555 1555 2.06 LINK OD2 ASP A 332 MN MN A 502 1555 1555 2.15 LINK OD1 ASP A 332 MN MN A 503 1555 1555 2.11 LINK OE1 GLU A 386 MN MN A 506 1555 1555 2.32 LINK OE2 GLU A 386 MN MN A 506 1555 1555 2.22 LINK OD2 ASP A 418 MN MN A 503 1555 1555 2.07 LINK NA NA A 501 O HOH A 819 1555 1555 2.33 LINK NA NA A 501 OP1 DT P 3 1555 1555 2.47 LINK NA NA A 501 O HOH P 216 1555 1555 2.34 LINK MN MN A 502 O2B DGT A 511 1555 1555 2.24 LINK MN MN A 502 O1G DGT A 511 1555 1555 2.11 LINK MN MN A 502 O HOH A 735 1555 1555 2.19 LINK MN MN A 502 OP1 DG P 5 1555 1555 2.27 LINK MN MN A 503 O3' DA P 4 1555 1555 2.61 LINK MN MN A 503 OP1 DG P 5 1555 1555 2.15 LINK MN MN A 503 O HOH P 202 1555 1555 2.23 LINK MN MN A 504 OP3 DG D 1 1555 1555 2.13 LINK MN MN A 504 O HOH D 208 1555 1555 2.32 LINK MN MN A 504 O HOH D 219 1555 1555 1.84 LINK MN MN A 506 O HOH A 817 1555 1555 2.23 LINK MN MN A 506 O AHOH A 841 1555 1555 2.25 LINK MN MN A 506 O HOH T 103 1555 1555 2.35 LINK O1B DGT A 511 MN MN P 101 1555 1555 2.08 LINK O HOH A 717 MN MN P 101 1555 1555 2.12 LINK OP2 DG P 5 MN MN P 101 1555 1555 2.10 LINK MN MN P 101 O HOH P 210 1555 1555 2.21 LINK MN MN P 101 O HOH P 212 1555 1555 1.72 LINK N7 DG D 1 MN MN D 101 1555 1555 2.42 LINK MN MN D 101 O HOH D 211 1555 1555 2.49 LINK MN MN D 101 O HOH D 214 1555 1555 2.49 CISPEP 1 GLY A 436 SER A 437 0 -7.52 CRYST1 59.893 68.866 110.319 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 0.016696 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014521 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009065 0.00000