HEADER REPLICATION 24-NOV-20 7KTJ TITLE DNA POLYMERASE MU (K438D), 8-OXODGTP:CT PRE-CATALYTIC GROUND STATE TITLE 2 TERNARY COMPLEX, 20 MM CA2+ (120MIN) 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 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*GP*TP*A)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*CP*CP*G)-3'); COMPND 18 CHAIN: D; COMPND 19 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 NUCLEOTIDE INSERTION, DNA KEYWDS 2 POLYMERASE MU, DOUBLE STRAND BREAK REPAIR, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JAMSEN,S.H.WILSON REVDAT 2 18-OCT-23 7KTJ 1 REMARK REVDAT 1 11-MAY-22 7KTJ 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 71980 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 3587 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 34.8550 - 4.2994 0.86 2652 137 0.1817 0.1817 REMARK 3 2 4.2994 - 3.4135 0.85 2550 125 0.1490 0.1912 REMARK 3 3 3.4135 - 2.9823 0.86 2502 128 0.1633 0.1633 REMARK 3 4 2.9823 - 2.7097 0.91 2619 164 0.1641 0.1971 REMARK 3 5 2.7097 - 2.5156 0.93 2717 126 0.1516 0.2133 REMARK 3 6 2.5156 - 2.3673 0.95 2747 144 0.1472 0.1559 REMARK 3 7 2.3673 - 2.2488 0.89 2565 138 0.1454 0.1686 REMARK 3 8 2.2488 - 2.1509 0.91 2579 150 0.1443 0.1771 REMARK 3 9 2.1509 - 2.0681 0.92 2660 133 0.1524 0.1570 REMARK 3 10 2.0681 - 1.9967 0.94 2698 132 0.1507 0.1810 REMARK 3 11 1.9967 - 1.9343 0.95 2698 147 0.1494 0.1672 REMARK 3 12 1.9343 - 1.8790 0.95 2710 133 0.1461 0.1670 REMARK 3 13 1.8790 - 1.8296 0.94 2693 145 0.1476 0.1845 REMARK 3 14 1.8296 - 1.7849 0.94 2678 144 0.1517 0.1897 REMARK 3 15 1.7849 - 1.7443 0.94 2684 142 0.1544 0.1739 REMARK 3 16 1.7443 - 1.7072 0.94 2685 140 0.1589 0.1800 REMARK 3 17 1.7072 - 1.6731 0.91 2584 135 0.1581 0.1986 REMARK 3 18 1.6731 - 1.6415 0.88 2498 131 0.1593 0.2153 REMARK 3 19 1.6415 - 1.6122 0.92 2636 129 0.1693 0.2006 REMARK 3 20 1.6122 - 1.5849 0.92 2625 134 0.1737 0.1737 REMARK 3 21 1.5849 - 1.5593 0.93 2618 145 0.1817 0.2427 REMARK 3 22 1.5593 - 1.5353 0.93 2627 134 0.1914 0.1922 REMARK 3 23 1.5353 - 1.5127 0.93 2662 133 0.2025 0.2437 REMARK 3 24 1.5127 - 1.4914 0.92 2630 140 0.2112 0.2444 REMARK 3 25 1.4914 - 1.4713 0.92 2591 134 0.2277 0.2402 REMARK 3 26 1.4713 - 1.4522 0.88 2485 144 0.2526 0.3076 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) : 16.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.32 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): 5.3100 -4.2494 -11.8354 REMARK 3 T TENSOR REMARK 3 T11: 0.1113 T22: 0.1227 REMARK 3 T33: 0.1056 T12: 0.0034 REMARK 3 T13: -0.0214 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.8519 L22: 0.9392 REMARK 3 L33: 0.9418 L12: -0.0434 REMARK 3 L13: -0.2395 L23: 0.2819 REMARK 3 S TENSOR REMARK 3 S11: 0.0255 S12: -0.0020 S13: -0.0180 REMARK 3 S21: 0.0576 S22: -0.0293 S23: -0.0677 REMARK 3 S31: -0.0506 S32: 0.0724 S33: 0.0007 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'T' AND RESID 1 THROUGH 9) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0922 -6.2499 -25.6783 REMARK 3 T TENSOR REMARK 3 T11: 0.2283 T22: 0.2034 REMARK 3 T33: 0.1635 T12: 0.0193 REMARK 3 T13: -0.0251 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 0.0035 L22: 0.1276 REMARK 3 L33: 0.0435 L12: 0.0221 REMARK 3 L13: -0.0133 L23: -0.0752 REMARK 3 S TENSOR REMARK 3 S11: 0.0914 S12: 0.0440 S13: -0.0404 REMARK 3 S21: -0.3673 S22: -0.1113 S23: 0.1551 REMARK 3 S31: -0.2208 S32: -0.0696 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'P' AND RESID 1 THROUGH 4) REMARK 3 ORIGIN FOR THE GROUP (A): 3.9941 4.1971 -19.2097 REMARK 3 T TENSOR REMARK 3 T11: 0.2426 T22: 0.2284 REMARK 3 T33: 0.1841 T12: -0.0152 REMARK 3 T13: -0.0185 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.0131 L22: 0.0046 REMARK 3 L33: 0.0067 L12: 0.0018 REMARK 3 L13: -0.0028 L23: 0.0035 REMARK 3 S TENSOR REMARK 3 S11: 0.0840 S12: 0.0887 S13: -0.2277 REMARK 3 S21: -0.0191 S22: -0.0100 S23: 0.0480 REMARK 3 S31: 0.1941 S32: 0.0768 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): 6.7179 -20.0321 -29.4644 REMARK 3 T TENSOR REMARK 3 T11: 0.1844 T22: 0.2245 REMARK 3 T33: 0.1844 T12: 0.0113 REMARK 3 T13: -0.0116 T23: -0.0313 REMARK 3 L TENSOR REMARK 3 L11: 0.0638 L22: 0.0649 REMARK 3 L33: 0.0779 L12: -0.0642 REMARK 3 L13: 0.0703 L23: -0.0712 REMARK 3 S TENSOR REMARK 3 S11: -0.0059 S12: -0.1096 S13: -0.0930 REMARK 3 S21: -0.0828 S22: 0.1614 S23: 0.0853 REMARK 3 S31: 0.1488 S32: -0.1550 S33: 0.0043 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 7KTJ 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_1000252987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-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 : 72011 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 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 (%) : 91.6 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.85400 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 (%): 49.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 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 30.01000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.10600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.04950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.10600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.01000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.04950 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: 6400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 GLN A 366 REMARK 465 HIS A 367 REMARK 465 SER A 368 REMARK 465 CYS A 369 REMARK 465 CYS A 370 REMARK 465 GLU A 371 REMARK 465 SER A 372 REMARK 465 PRO A 373 REMARK 465 THR A 374 REMARK 465 ARG A 375 REMARK 465 LEU A 376 REMARK 465 ALA A 377 REMARK 465 GLN A 378 REMARK 465 GLN A 379 REMARK 465 SER A 380 REMARK 465 HIS A 381 REMARK 465 MET A 382 REMARK 465 ASP A 383 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TRP A 137 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 137 CZ3 CH2 REMARK 470 GLU A 170 CD OE1 OE2 REMARK 470 LEU A 196 CG CD1 CD2 REMARK 470 GLN A 200 CD OE1 NE2 REMARK 470 GLU A 207 CD OE1 OE2 REMARK 470 GLU A 267 CD OE1 OE2 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 284 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 CE NZ REMARK 470 GLN A 355 CG CD OE1 NE2 REMARK 470 GLN A 357 CG CD OE1 NE2 REMARK 470 HIS A 365 ND1 CE1 NE2 REMARK 470 GLN A 466 OE1 NE2 REMARK 470 ARG A 480 NH1 NH2 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' -0.036 REMARK 500 DG D 1 P DG D 1 OP3 -0.124 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 - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 438 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 DA T 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DA T 7 O4' - C1' - N9 ANGL. DEV. = 3.5 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 LEU A 310 103.90 -161.86 REMARK 500 THR A 318 -148.72 -120.66 REMARK 500 THR A 318 -152.22 -124.83 REMARK 500 SER A 411 -150.22 -165.58 REMARK 500 ASN A 493 47.76 -86.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC T 1 0.06 SIDE CHAIN 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 511 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 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 205 O REMARK 620 2 HOH A 812 O 89.4 REMARK 620 3 HOH A 898 O 148.8 102.4 REMARK 620 4 HOH D 103 O 75.0 154.0 82.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 91.8 REMARK 620 3 VAL A 246 O 83.1 88.7 REMARK 620 4 DT P 3 OP1 169.8 90.7 87.0 REMARK 620 5 HOH P 109 O 110.5 90.0 166.3 79.4 REMARK 620 6 HOH P 110 O 88.3 166.1 77.6 86.9 103.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 330 OD2 50.7 REMARK 620 3 ASP A 332 OD1 81.8 127.1 REMARK 620 4 ASP A 418 OD2 106.8 82.4 92.4 REMARK 620 5 8DG A 506 O2A 68.5 90.5 92.2 172.9 REMARK 620 6 HOH A 744 O 164.9 143.1 83.1 74.9 111.0 REMARK 620 7 HOH P 102 O 119.9 76.9 156.0 90.9 87.2 74.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 O REMARK 620 2 ASP A 330 OD1 67.0 REMARK 620 3 ASP A 332 OD2 95.7 86.4 REMARK 620 4 8DG A 506 O2B 140.3 152.4 92.6 REMARK 620 5 8DG A 506 O2A 140.3 74.3 90.4 78.1 REMARK 620 6 8DG A 506 O2G 84.6 103.9 168.9 80.3 96.5 REMARK 620 7 HOH A 743 O 64.3 129.1 84.4 78.1 155.3 85.7 REMARK 620 N 1 2 3 4 5 6 DBREF 7KTJ A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 7KTJ T 1 9 PDB 7KTJ 7KTJ 1 9 DBREF 7KTJ P 1 4 PDB 7KTJ 7KTJ 1 4 DBREF 7KTJ D 1 4 PDB 7KTJ 7KTJ 1 4 SEQADV 7KTJ GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 7KTJ SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 7KTJ ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 7KTJ ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 7KTJ ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 7KTJ A UNP Q9NP87 PRO 398 DELETION SEQADV 7KTJ A UNP Q9NP87 GLY 399 DELETION SEQADV 7KTJ A UNP Q9NP87 ALA 400 DELETION SEQADV 7KTJ A UNP Q9NP87 ALA 401 DELETION SEQADV 7KTJ A UNP Q9NP87 VAL 402 DELETION SEQADV 7KTJ A UNP Q9NP87 GLY 403 DELETION SEQADV 7KTJ A UNP Q9NP87 GLY 404 DELETION SEQADV 7KTJ A UNP Q9NP87 SER 405 DELETION SEQADV 7KTJ A UNP Q9NP87 THR 406 DELETION SEQADV 7KTJ A UNP Q9NP87 ARG 407 DELETION SEQADV 7KTJ A UNP Q9NP87 PRO 408 DELETION SEQADV 7KTJ A UNP Q9NP87 CYS 409 DELETION SEQADV 7KTJ GLY A 410 UNP Q9NP87 PRO 410 CONFLICT SEQADV 7KTJ ASP A 438 UNP Q9NP87 LYS 438 ENGINEERED MUTATION 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 ASP 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 CA A 501 1 HET CA A 502 1 HET CA A 503 1 HET NA A 504 1 HET CL A 505 1 HET 8DG A 506 32 HET EPE A 507 5 HET EDO A 508 4 HET EDO A 509 4 HET EDO A 510 8 HET EDO A 511 2 HET EDO T 101 8 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 5 CA 3(CA 2+) FORMUL 8 NA NA 1+ FORMUL 9 CL CL 1- FORMUL 10 8DG C10 H16 N5 O14 P3 FORMUL 11 EPE C8 H18 N2 O4 S FORMUL 12 EDO 5(C2 H6 O2) FORMUL 17 HOH *383(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 ARG A 230 1 9 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 O PHE A 205 NA NA A 504 1555 1555 2.24 LINK O THR A 241 CA CA A 503 1555 1555 2.33 LINK O ILE A 243 CA CA A 503 1555 1555 2.42 LINK O VAL A 246 CA CA A 503 1555 1555 2.32 LINK OD1 ASP A 330 CA CA A 501 1555 1555 2.63 LINK OD2 ASP A 330 CA CA A 501 1555 1555 2.43 LINK O ASP A 330 CA CA A 502 1555 1555 2.79 LINK OD1 ASP A 330 CA CA A 502 1555 1555 2.29 LINK OD1 ASP A 332 CA CA A 501 1555 1555 2.36 LINK OD2 ASP A 332 CA CA A 502 1555 1555 2.33 LINK OD2 ASP A 418 CA CA A 501 1555 1555 2.26 LINK CA CA A 501 O2A 8DG A 506 1555 1555 2.43 LINK CA CA A 501 O HOH A 744 1555 1555 2.35 LINK CA CA A 501 O HOH P 102 1555 1555 2.37 LINK CA CA A 502 O2B 8DG A 506 1555 1555 2.34 LINK CA CA A 502 O2A 8DG A 506 1555 1555 2.43 LINK CA CA A 502 O2G 8DG A 506 1555 1555 2.32 LINK CA CA A 502 O HOH A 743 1555 1555 2.45 LINK CA CA A 503 OP1 DT P 3 1555 1555 2.53 LINK CA CA A 503 O HOH P 109 1555 1555 2.33 LINK CA CA A 503 O HOH P 110 1555 1555 2.45 LINK NA NA A 504 O HOH A 812 1555 1555 2.24 LINK NA NA A 504 O HOH A 898 1555 1555 2.27 LINK NA NA A 504 O HOH D 103 1555 1555 2.63 CISPEP 1 GLY A 436 SER A 437 0 -6.60 CRYST1 60.020 62.099 118.212 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 0.016661 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008459 0.00000