HEADER HYDROLASE/DNA 04-AUG-20 7COC TITLE TERNARY COMPLEX OF DNA POLYMERASE MU (K438A/Q441A) WITH 1-NT GAPPED TITLE 2 DNA (T:DGMPNPP) 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*TP*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; COMPND 20 OTHER_DETAILS: 5' PHOSPHORYLATED DG 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: PET28A; 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 POLYMERASE MU, MISINCORPORATION, GAP FILLING, MUTAGENESIS, HYDROLASE, KEYWDS 2 HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.GUO,Y.ZHAO REVDAT 2 29-NOV-23 7COC 1 REMARK REVDAT 1 30-JUN-21 7COC 0 JRNL AUTH M.GUO,Y.WANG,Y.TANG,Z.CHEN,J.HOU,J.DAI,Y.WANG,L.WANG,H.XU, JRNL AUTH 2 B.TIAN,Y.HUA,Y.ZHAO JRNL TITL MECHANISM OF GENOME INSTABILITY MEDIATED BY HUMAN DNA JRNL TITL 2 POLYMERASE MU MISINCORPORATION. JRNL REF NAT COMMUN V. 12 3759 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34145298 JRNL DOI 10.1038/S41467-021-24096-7 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 36234 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1801 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 29.1320 - 4.4609 0.97 2773 143 0.1546 0.1821 REMARK 3 2 4.4609 - 3.5428 0.98 2666 135 0.1506 0.1666 REMARK 3 3 3.5428 - 3.0955 0.98 2646 137 0.1785 0.2182 REMARK 3 4 3.0955 - 2.8127 0.99 2679 130 0.2076 0.2154 REMARK 3 5 2.8127 - 2.6113 0.99 2641 155 0.2014 0.2459 REMARK 3 6 2.6113 - 2.4574 1.00 2627 142 0.2009 0.2329 REMARK 3 7 2.4574 - 2.3344 1.00 2676 142 0.1901 0.2204 REMARK 3 8 2.3344 - 2.2328 0.99 2640 111 0.2060 0.2235 REMARK 3 9 2.2328 - 2.1469 1.00 2633 156 0.1963 0.2437 REMARK 3 10 2.1469 - 2.0728 1.00 2619 141 0.1997 0.2789 REMARK 3 11 2.0728 - 2.0080 1.00 2637 140 0.2144 0.2384 REMARK 3 12 2.0080 - 1.9506 1.00 2663 132 0.2250 0.2503 REMARK 3 13 1.9506 - 1.9000 0.97 2533 137 0.2798 0.3265 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.59 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: CHAIN A OR CHAIN T OR CHAIN P OR CHAIN D REMARK 3 ORIGIN FOR THE GROUP (A): 3.3254 3.6510 11.7670 REMARK 3 T TENSOR REMARK 3 T11: 0.1708 T22: 0.1731 REMARK 3 T33: 0.1652 T12: -0.0029 REMARK 3 T13: 0.0001 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.3863 L22: 0.2734 REMARK 3 L33: 0.3411 L12: 0.0454 REMARK 3 L13: 0.0556 L23: -0.0441 REMARK 3 S TENSOR REMARK 3 S11: 0.0440 S12: -0.0487 S13: -0.0171 REMARK 3 S21: 0.0213 S22: -0.0358 S23: -0.0061 REMARK 3 S31: -0.0047 S32: -0.0084 S33: -0.0000 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 7COC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1300017970. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36257 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.899 REMARK 200 RESOLUTION RANGE LOW (A) : 29.132 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.459 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.60400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4M04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEXYLENE GLYCOL, HEPES, PEG10000, PH REMARK 280 7.5, VAPOR DIFFUSION, TEMPERATURE 298K 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 29.98000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.27000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.27000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.98000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.28000 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: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 MET A 1 REMARK 465 LEU A 2 REMARK 465 PRO A 3 REMARK 465 LYS A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 6 REMARK 465 ARG A 7 REMARK 465 ALA A 8 REMARK 465 ARG A 9 REMARK 465 VAL A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 PRO A 13 REMARK 465 SER A 14 REMARK 465 GLY A 15 REMARK 465 ASP A 16 REMARK 465 ALA A 17 REMARK 465 ALA A 18 REMARK 465 SER A 19 REMARK 465 SER A 20 REMARK 465 THR A 21 REMARK 465 PRO A 22 REMARK 465 PRO A 23 REMARK 465 SER A 24 REMARK 465 THR A 25 REMARK 465 ARG A 26 REMARK 465 PHE A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 VAL A 30 REMARK 465 ALA A 31 REMARK 465 ILE A 32 REMARK 465 TYR A 33 REMARK 465 LEU A 34 REMARK 465 VAL A 35 REMARK 465 GLU A 36 REMARK 465 PRO A 37 REMARK 465 ARG A 38 REMARK 465 MET A 39 REMARK 465 GLY A 40 REMARK 465 ARG A 41 REMARK 465 SER A 42 REMARK 465 ARG A 43 REMARK 465 ARG A 44 REMARK 465 ALA A 45 REMARK 465 PHE A 46 REMARK 465 LEU A 47 REMARK 465 THR A 48 REMARK 465 GLY A 49 REMARK 465 LEU A 50 REMARK 465 ALA A 51 REMARK 465 ARG A 52 REMARK 465 SER A 53 REMARK 465 LYS A 54 REMARK 465 GLY A 55 REMARK 465 PHE A 56 REMARK 465 ARG A 57 REMARK 465 VAL A 58 REMARK 465 LEU A 59 REMARK 465 ASP A 60 REMARK 465 ALA A 61 REMARK 465 CYS A 62 REMARK 465 SER A 63 REMARK 465 SER A 64 REMARK 465 GLU A 65 REMARK 465 ALA A 66 REMARK 465 THR A 67 REMARK 465 HIS A 68 REMARK 465 VAL A 69 REMARK 465 VAL A 70 REMARK 465 MET A 71 REMARK 465 GLU A 72 REMARK 465 GLU A 73 REMARK 465 THR A 74 REMARK 465 SER A 75 REMARK 465 ALA A 76 REMARK 465 GLU A 77 REMARK 465 GLU A 78 REMARK 465 ALA A 79 REMARK 465 VAL A 80 REMARK 465 SER A 81 REMARK 465 TRP A 82 REMARK 465 GLN A 83 REMARK 465 GLU A 84 REMARK 465 ARG A 85 REMARK 465 ARG A 86 REMARK 465 MET A 87 REMARK 465 ALA A 88 REMARK 465 ALA A 89 REMARK 465 ALA A 90 REMARK 465 PRO A 91 REMARK 465 PRO A 92 REMARK 465 GLY A 93 REMARK 465 CYS A 94 REMARK 465 THR A 95 REMARK 465 PRO A 96 REMARK 465 PRO A 97 REMARK 465 ALA A 98 REMARK 465 LEU A 99 REMARK 465 LEU A 100 REMARK 465 ASP A 101 REMARK 465 ILE A 102 REMARK 465 SER A 103 REMARK 465 TRP A 104 REMARK 465 LEU A 105 REMARK 465 THR A 106 REMARK 465 GLU A 107 REMARK 465 SER A 108 REMARK 465 LEU A 109 REMARK 465 GLY A 110 REMARK 465 ALA A 111 REMARK 465 GLY A 112 REMARK 465 GLN A 113 REMARK 465 PRO A 114 REMARK 465 VAL A 115 REMARK 465 PRO A 116 REMARK 465 VAL A 117 REMARK 465 GLU A 118 REMARK 465 CYS A 119 REMARK 465 ARG A 120 REMARK 465 HIS A 121 REMARK 465 ARG A 122 REMARK 465 LEU A 123 REMARK 465 GLU A 124 REMARK 465 VAL A 125 REMARK 465 ALA A 126 REMARK 465 GLY A 127 REMARK 465 PRO A 128 REMARK 465 ARG A 129 REMARK 465 LYS A 130 REMARK 465 GLY 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 MET A 138 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 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 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 DT T 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 153 40.72 -140.26 REMARK 500 THR A 318 -154.59 -124.98 REMARK 500 THR A 318 -157.17 -128.69 REMARK 500 ASN A 493 47.48 -87.18 REMARK 500 REMARK 500 REMARK: NULL 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 K A 504 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 93.3 REMARK 620 3 VAL A 246 O 79.7 86.5 REMARK 620 4 DT P 3 OP1 169.9 91.0 91.4 REMARK 620 5 HOH P 101 O 86.2 156.2 70.0 86.2 REMARK 620 6 HOH P 104 O 104.6 98.6 173.0 83.8 104.6 REMARK 620 N 1 2 3 4 5 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 OD2 REMARK 620 2 ASP A 332 OD1 95.7 REMARK 620 3 ASP A 418 OD2 83.8 94.6 REMARK 620 4 XG4 A 501 O1A 98.7 91.8 172.9 REMARK 620 5 HOH A 682 O 167.4 84.6 83.6 93.9 REMARK 620 6 HOH P 102 O 93.0 171.3 85.4 87.8 86.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD1 REMARK 620 2 ASP A 332 OD2 94.7 REMARK 620 3 XG4 A 501 O1A 94.3 87.3 REMARK 620 4 XG4 A 501 O1B 172.9 92.2 87.8 REMARK 620 5 XG4 A 501 O1G 84.8 178.3 94.3 88.2 REMARK 620 6 HOH A 658 O 86.8 87.5 174.8 91.7 90.9 REMARK 620 N 1 2 3 4 5 DBREF 7COC A 1 494 UNP Q9NP87 DPOLM_HUMAN 1 494 DBREF 7COC T 1 9 PDB 7COC 7COC 1 9 DBREF 7COC P 1 4 PDB 7COC 7COC 1 4 DBREF 7COC D 1 4 PDB 7COC 7COC 1 4 SEQADV 7COC A UNP Q9NP87 PRO 398 DELETION SEQADV 7COC A UNP Q9NP87 GLY 399 DELETION SEQADV 7COC A UNP Q9NP87 ALA 400 DELETION SEQADV 7COC A UNP Q9NP87 ALA 401 DELETION SEQADV 7COC A UNP Q9NP87 VAL 402 DELETION SEQADV 7COC A UNP Q9NP87 GLY 403 DELETION SEQADV 7COC A UNP Q9NP87 GLY 404 DELETION SEQADV 7COC A UNP Q9NP87 SER 405 DELETION SEQADV 7COC A UNP Q9NP87 THR 406 DELETION SEQADV 7COC A UNP Q9NP87 ARG 407 DELETION SEQADV 7COC A UNP Q9NP87 PRO 408 DELETION SEQADV 7COC A UNP Q9NP87 CYS 409 DELETION SEQADV 7COC GLY A 410 UNP Q9NP87 PRO 410 ENGINEERED MUTATION SEQADV 7COC ALA A 438 UNP Q9NP87 LYS 438 ENGINEERED MUTATION SEQADV 7COC ALA A 441 UNP Q9NP87 GLN 441 ENGINEERED MUTATION SEQRES 1 A 482 MET LEU PRO LYS ARG ARG ARG ALA ARG VAL GLY SER PRO SEQRES 2 A 482 SER GLY ASP ALA ALA SER SER THR PRO PRO SER THR ARG SEQRES 3 A 482 PHE PRO GLY VAL ALA ILE TYR LEU VAL GLU PRO ARG MET SEQRES 4 A 482 GLY ARG SER ARG ARG ALA PHE LEU THR GLY LEU ALA ARG SEQRES 5 A 482 SER LYS GLY PHE ARG VAL LEU ASP ALA CYS SER SER GLU SEQRES 6 A 482 ALA THR HIS VAL VAL MET GLU GLU THR SER ALA GLU GLU SEQRES 7 A 482 ALA VAL SER TRP GLN GLU ARG ARG MET ALA ALA ALA PRO SEQRES 8 A 482 PRO GLY CYS THR PRO PRO ALA LEU LEU ASP ILE SER TRP SEQRES 9 A 482 LEU THR GLU SER LEU GLY ALA GLY GLN PRO VAL PRO VAL SEQRES 10 A 482 GLU CYS ARG HIS ARG LEU GLU VAL ALA GLY PRO ARG LYS SEQRES 11 A 482 GLY PRO LEU SER PRO ALA TRP MET PRO ALA TYR ALA CYS SEQRES 12 A 482 GLN ARG PRO THR PRO LEU THR HIS HIS ASN THR GLY LEU SEQRES 13 A 482 SER GLU ALA LEU GLU ILE LEU ALA GLU ALA ALA GLY PHE SEQRES 14 A 482 GLU GLY SER GLU GLY ARG LEU LEU THR PHE CYS ARG ALA SEQRES 15 A 482 ALA SER VAL LEU LYS ALA LEU PRO SER PRO VAL THR THR SEQRES 16 A 482 LEU SER GLN LEU GLN GLY LEU PRO HIS PHE GLY GLU HIS SEQRES 17 A 482 SER SER ARG VAL VAL GLN GLU LEU LEU GLU HIS GLY VAL SEQRES 18 A 482 CYS GLU GLU VAL GLU ARG VAL ARG ARG SER GLU ARG TYR SEQRES 19 A 482 GLN THR MET LYS LEU PHE THR GLN ILE PHE GLY VAL GLY SEQRES 20 A 482 VAL LYS THR ALA ASP ARG TRP TYR ARG GLU GLY LEU ARG SEQRES 21 A 482 THR LEU ASP ASP LEU ARG GLU GLN PRO GLN LYS LEU THR SEQRES 22 A 482 GLN GLN GLN LYS ALA GLY LEU GLN HIS HIS GLN ASP LEU SEQRES 23 A 482 SER THR PRO VAL LEU ARG SER ASP VAL ASP ALA LEU GLN SEQRES 24 A 482 GLN VAL VAL GLU GLU ALA VAL GLY GLN ALA LEU PRO GLY SEQRES 25 A 482 ALA THR VAL THR LEU THR GLY GLY PHE ARG ARG GLY LYS SEQRES 26 A 482 LEU GLN GLY HIS ASP VAL ASP PHE LEU ILE THR HIS PRO SEQRES 27 A 482 LYS GLU GLY GLN GLU ALA GLY LEU LEU PRO ARG VAL MET SEQRES 28 A 482 CYS ARG LEU GLN ASP GLN GLY LEU ILE LEU TYR HIS GLN SEQRES 29 A 482 HIS GLN HIS SER CYS CYS GLU SER PRO THR ARG LEU ALA SEQRES 30 A 482 GLN GLN SER HIS MET ASP ALA PHE GLU ARG SER PHE CYS SEQRES 31 A 482 ILE PHE ARG LEU PRO GLN PRO GLY SER TRP LYS ALA VAL SEQRES 32 A 482 ARG VAL ASP LEU VAL VAL ALA PRO VAL SER GLN PHE PRO SEQRES 33 A 482 PHE ALA LEU LEU GLY TRP THR GLY SER ALA LEU PHE ALA SEQRES 34 A 482 ARG GLU LEU ARG ARG PHE SER ARG LYS GLU LYS GLY LEU SEQRES 35 A 482 TRP LEU ASN SER HIS GLY LEU PHE ASP PRO GLU GLN LYS SEQRES 36 A 482 THR PHE PHE GLN ALA ALA SER GLU GLU ASP ILE PHE ARG SEQRES 37 A 482 HIS LEU GLY LEU GLU TYR LEU PRO PRO GLU GLN ARG ASN SEQRES 38 A 482 ALA SEQRES 1 T 9 DC DG DG DC DT DT DA DC DG SEQRES 1 P 4 DC DG DT DA SEQRES 1 D 4 DG DC DC DG HET XG4 A 501 31 HET MG A 502 1 HET MG A 503 1 HET K A 504 1 HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 5 XG4 C10 H17 N6 O12 P3 FORMUL 6 MG 2(MG 2+) FORMUL 8 K K 1+ FORMUL 9 HOH *256(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 VAL A 331 THR A 336 -1 O LEU A 334 N THR A 316 SHEET 3 AA2 5 TRP A 412 VAL A 421 1 O VAL A 420 N ILE A 335 SHEET 4 AA2 5 ARG A 387 PRO A 395 -1 N PHE A 392 O VAL A 415 SHEET 5 AA2 5 ILE A 360 TYR A 362 -1 N LEU A 361 O ILE A 391 SHEET 1 AA3 3 TRP A 455 LEU A 456 0 SHEET 2 AA3 3 LEU A 461 ASP A 463 -1 O PHE A 462 N TRP A 455 SHEET 3 AA3 3 THR A 468 PHE A 469 -1 O THR A 468 N ASP A 463 LINK O THR A 241 K K A 504 1555 1555 2.52 LINK O ILE A 243 K K A 504 1555 1555 2.62 LINK O VAL A 246 K K A 504 1555 1555 2.61 LINK OD2 ASP A 330 MG MG A 502 1555 1555 2.22 LINK OD1 ASP A 330 MG MG A 503 1555 1555 2.19 LINK OD1 ASP A 332 MG MG A 502 1555 1555 2.04 LINK OD2 ASP A 332 MG MG A 503 1555 1555 2.03 LINK OD2 ASP A 418 MG MG A 502 1555 1555 2.11 LINK O1A XG4 A 501 MG MG A 502 1555 1555 2.22 LINK O1A XG4 A 501 MG MG A 503 1555 1555 2.22 LINK O1B XG4 A 501 MG MG A 503 1555 1555 2.22 LINK O1G XG4 A 501 MG MG A 503 1555 1555 2.22 LINK MG MG A 502 O HOH A 682 1555 1555 2.10 LINK MG MG A 502 O HOH P 102 1555 1555 2.21 LINK MG MG A 503 O HOH A 658 1555 1555 2.08 LINK K K A 504 OP1 DT P 3 1555 1555 2.58 LINK K K A 504 O HOH P 101 1555 1555 2.78 LINK K K A 504 O HOH P 104 1555 1555 2.47 CISPEP 1 GLY A 436 SER A 437 0 -1.36 CRYST1 59.960 68.560 110.540 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 0.016678 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009046 0.00000