HEADER TRANSFERASE/DNA 21-NOV-16 5TYV TITLE DNA POLYMERASE MU REACTANT COMPLEX, MN2+ (7.5 MIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-DIRECTED DNA/RNA POLYMERASE MU; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 132-494; COMPND 5 SYNONYM: POL MU,TERMINAL TRANSFERASE; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*CP*GP*GP*CP*AP*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*AP*T)-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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: CODONPLUS-RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEXM; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 15 ORGANISM_TAXID: 32644; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 19 ORGANISM_TAXID: 32644; SOURCE 20 MOL_ID: 4; SOURCE 21 SYNTHETIC: YES; SOURCE 22 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 23 ORGANISM_TAXID: 32644 KEYWDS TIME-LAPSE CRYSTALLOGRAPHY, PRODUCT METAL, DNA POLYMERASE MU, DOUBLE KEYWDS 2 STRAND BREAK REPAIR, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JAMSEN,S.H.WILSON REVDAT 4 04-OCT-23 5TYV 1 LINK REVDAT 3 18-DEC-19 5TYV 1 REMARK REVDAT 2 27-SEP-17 5TYV 1 REMARK REVDAT 1 30-AUG-17 5TYV 0 JRNL AUTH J.A.JAMSEN,W.A.BEARD,L.C.PEDERSEN,D.D.SHOCK,A.F.MOON, JRNL AUTH 2 J.M.KRAHN,K.BEBENEK,T.A.KUNKEL,S.H.WILSON JRNL TITL TIME-LAPSE CRYSTALLOGRAPHY SNAPSHOTS OF A DOUBLE-STRAND JRNL TITL 2 BREAK REPAIR POLYMERASE IN ACTION. JRNL REF NAT COMMUN V. 8 253 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28811466 JRNL DOI 10.1038/S41467-017-00271-7 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 34504 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1722 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 23.2076 - 4.4097 0.99 2924 155 0.1756 0.1985 REMARK 3 2 4.4097 - 3.5040 1.00 2794 148 0.1535 0.1689 REMARK 3 3 3.5040 - 3.0622 1.00 2791 147 0.1750 0.2006 REMARK 3 4 3.0622 - 2.7827 0.97 2682 140 0.2265 0.2393 REMARK 3 5 2.7827 - 2.5835 0.99 2725 143 0.2235 0.2545 REMARK 3 6 2.5835 - 2.4314 1.00 2734 144 0.2076 0.2489 REMARK 3 7 2.4314 - 2.3097 1.00 2710 140 0.1987 0.2427 REMARK 3 8 2.3097 - 2.2093 1.00 2749 146 0.1976 0.2728 REMARK 3 9 2.2093 - 2.1243 1.00 2718 146 0.1929 0.2453 REMARK 3 10 2.1243 - 2.0510 1.00 2725 141 0.1950 0.2343 REMARK 3 11 2.0510 - 1.9869 0.99 2676 141 0.2171 0.2488 REMARK 3 12 1.9869 - 1.9302 0.94 2554 131 0.2838 0.3057 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) : 22.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.66 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 : 0.003 3295 REMARK 3 ANGLE : 0.541 4581 REMARK 3 CHIRALITY : 0.040 497 REMARK 3 PLANARITY : 0.003 527 REMARK 3 DIHEDRAL : 12.048 1033 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5TYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1000225052. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34708 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.74600 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 (%): 53.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 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 29.97350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.99700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.37600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.99700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.97350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.37600 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: 7410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 GLN A 200 CD OE1 NE2 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 GLN A 364 CG CD OE1 NE2 REMARK 470 LYS A 467 CD CE NZ 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 DG D 1 P DG D 1 OP3 -0.128 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 6 O4' - C1' - N1 ANGL. DEV. = 2.1 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 42.54 -142.20 REMARK 500 THR A 318 -150.27 -125.55 REMARK 500 THR A 318 -157.35 -130.76 REMARK 500 PRO A 397 104.03 -47.62 REMARK 500 SER A 411 -144.45 -168.60 REMARK 500 ASN A 493 49.19 -84.92 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 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 506 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 208 ND1 REMARK 620 2 HOH A 833 O 95.9 REMARK 620 3 DG D 1 OP3 65.9 150.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 505 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 218 OE1 REMARK 620 2 HIS A 219 NE2 88.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 507 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 97.6 REMARK 620 3 VAL A 246 O 85.0 96.2 REMARK 620 4 HOH A 826 O 91.0 93.4 170.0 REMARK 620 5 DT P 3 OP1 171.5 90.5 91.9 90.8 REMARK 620 6 HOH P 214 O 86.7 175.6 84.4 86.2 85.1 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 97.0 REMARK 620 3 TTP A 501 O1A 94.2 97.1 REMARK 620 4 TTP A 501 O1B 170.6 91.8 81.4 REMARK 620 5 TTP A 501 O1G 85.7 177.1 83.6 85.5 REMARK 620 6 PPV A 511 O21 159.6 97.6 98.0 18.4 79.6 REMARK 620 7 PPV A 511 O32 81.9 177.2 85.6 89.4 4.2 82.8 REMARK 620 8 HOH A 662 O 86.2 86.5 176.3 97.7 92.8 80.6 90.8 REMARK 620 9 DT P 5 OP1 87.7 85.6 14.0 89.7 95.4 107.5 97.0 169.3 REMARK 620 N 1 2 3 4 5 6 7 8 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 96.8 REMARK 620 3 ASP A 418 OD2 90.2 94.4 REMARK 620 4 TTP A 501 O1A 103.1 91.7 164.6 REMARK 620 5 DA P 4 O3' 171.8 90.8 86.0 79.8 REMARK 620 6 DA P 4 O3' 165.5 97.4 91.6 73.5 9.1 REMARK 620 7 DT P 5 OP1 114.1 93.4 153.3 11.4 68.5 62.1 REMARK 620 8 HOH P 204 O 87.0 172.3 92.2 80.9 85.9 78.6 79.0 REMARK 620 N 1 2 3 4 5 6 7 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 GLU A 386 OE1 REMARK 620 2 GLU A 386 OE2 52.3 REMARK 620 3 HIS A 459 NE2 137.8 85.5 REMARK 620 4 HOH A 791 O 85.4 101.0 104.0 REMARK 620 5 HOH A 840 O 129.0 177.6 93.1 81.3 REMARK 620 6 HOH T 202 O 96.2 95.5 88.0 160.2 82.4 REMARK 620 N 1 2 3 4 5 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 PPV A 511 O31 REMARK 620 2 HOH A 609 O 91.9 REMARK 620 3 HOH A 785 O 104.4 87.6 REMARK 620 4 HOH A 800 O 84.2 86.9 169.9 REMARK 620 5 DT P 5 OP2 98.6 167.0 82.4 101.7 REMARK 620 6 HOH P 216 O 175.6 84.0 73.9 97.1 85.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN T 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG T 2 N7 REMARK 620 2 HOH T 201 O 85.2 REMARK 620 3 HOH T 203 O 88.9 78.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TTP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN T 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO P 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TXX RELATED DB: PDB REMARK 900 RELATED ID: 5TXZ RELATED DB: PDB REMARK 900 RELATED ID: 5TYB RELATED DB: PDB REMARK 900 RELATED ID: 5TYC RELATED DB: PDB REMARK 900 RELATED ID: 5TYD RELATED DB: PDB REMARK 900 RELATED ID: 5TYE RELATED DB: PDB REMARK 900 RELATED ID: 5TYF RELATED DB: PDB REMARK 900 RELATED ID: 5TYG RELATED DB: PDB REMARK 900 RELATED ID: 5TYU RELATED DB: PDB REMARK 900 RELATED ID: 5TYW RELATED DB: PDB REMARK 900 RELATED ID: 5TYX RELATED DB: PDB REMARK 900 RELATED ID: 5TYY RELATED DB: PDB REMARK 900 RELATED ID: 5TYZ RELATED DB: PDB DBREF 5TYV A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 5TYV T 1 9 PDB 5TYV 5TYV 1 9 DBREF 5TYV P 1 5 PDB 5TYV 5TYV 1 5 DBREF 5TYV D 1 4 PDB 5TYV 5TYV 1 4 SEQADV 5TYV GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYV SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYV ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYV ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYV ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYV A UNP Q9NP87 PRO 398 DELETION SEQADV 5TYV A UNP Q9NP87 GLY 399 DELETION SEQADV 5TYV A UNP Q9NP87 ALA 400 DELETION SEQADV 5TYV A UNP Q9NP87 ALA 401 DELETION SEQADV 5TYV A UNP Q9NP87 VAL 402 DELETION SEQADV 5TYV A UNP Q9NP87 GLY 403 DELETION SEQADV 5TYV A UNP Q9NP87 GLY 404 DELETION SEQADV 5TYV A UNP Q9NP87 SER 405 DELETION SEQADV 5TYV A UNP Q9NP87 THR 406 DELETION SEQADV 5TYV A UNP Q9NP87 ARG 407 DELETION SEQADV 5TYV A UNP Q9NP87 PRO 408 DELETION SEQADV 5TYV A UNP Q9NP87 CYS 409 DELETION SEQADV 5TYV 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 DT SEQRES 1 D 4 DG DC DC DG HET TTP A 501 29 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 NA A 507 1 HET EDO A 508 4 HET EDO A 509 4 HET EPE A 510 5 HET PPV A 511 9 HET MN T 101 1 HET MN P 101 1 HET EDO P 102 4 HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM PPV PYROPHOSPHATE HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 5 TTP C10 H17 N2 O14 P3 FORMUL 6 MN 7(MN 2+) FORMUL 11 NA NA 1+ FORMUL 12 EDO 3(C2 H6 O2) FORMUL 14 EPE C8 H18 N2 O4 S FORMUL 15 PPV H4 O7 P2 FORMUL 19 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 GLN A 426 GLY A 436 1 11 HELIX 17 AB8 SER A 437 GLY A 453 1 17 HELIX 18 AB9 SER A 474 LEU A 482 1 9 HELIX 19 AC1 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 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 ND1 HIS A 208 MN MN A 506 1555 1555 2.70 LINK OE1 GLU A 218 MN MN A 505 1555 1555 2.80 LINK NE2 HIS A 219 MN MN A 505 1555 1555 2.36 LINK O THR A 241 NA NA A 507 1555 1555 2.30 LINK O ILE A 243 NA NA A 507 1555 1555 2.32 LINK O VAL A 246 NA NA A 507 1555 1555 2.29 LINK OD1 ASP A 330 MN MN A 502 1555 1555 2.12 LINK OD2 ASP A 330 MN MN A 503 1555 1555 1.94 LINK OD2 ASP A 332 MN MN A 502 1555 1555 2.13 LINK OD1 ASP A 332 MN MN A 503 1555 1555 2.13 LINK OE1 GLU A 386 MN MN A 504 1555 1555 2.62 LINK OE2 GLU A 386 MN MN A 504 1555 1555 2.32 LINK OD2 ASP A 418 MN MN A 503 1555 1555 2.08 LINK NE2 HIS A 459 MN MN A 504 1555 1555 2.78 LINK O1AATTP A 501 MN MN A 502 1555 1555 1.83 LINK O1BATTP A 501 MN MN A 502 1555 1555 2.17 LINK O1GATTP A 501 MN MN A 502 1555 1555 2.18 LINK O1AATTP A 501 MN MN A 503 1555 1555 2.65 LINK MN MN A 502 O21BPPV A 511 1555 1555 2.16 LINK MN MN A 502 O32BPPV A 511 1555 1555 2.36 LINK MN MN A 502 O HOH A 662 1555 1555 1.98 LINK MN MN A 502 OP1B DT P 5 1555 1555 2.39 LINK MN MN A 503 O3'A DA P 4 1555 1555 2.72 LINK MN MN A 503 O3'B DA P 4 1555 1555 2.65 LINK MN MN A 503 OP1B DT P 5 1555 1555 2.06 LINK MN MN A 503 O HOH P 204 1555 1555 2.36 LINK MN MN A 504 O HOH A 791 1555 1555 2.53 LINK MN MN A 504 O HOH A 840 1555 1555 2.64 LINK MN MN A 504 O HOH T 202 1555 1555 2.38 LINK MN MN A 506 O AHOH A 833 1555 1555 2.20 LINK MN MN A 506 OP3 DG D 1 1555 1555 2.26 LINK NA NA A 507 O HOH A 826 1555 1555 2.47 LINK NA NA A 507 OP1 DT P 3 1555 1555 2.56 LINK NA NA A 507 O HOH P 214 1555 1555 2.48 LINK O31BPPV A 511 MN B MN P 101 1555 1555 2.37 LINK O BHOH A 609 MN B MN P 101 1555 1555 2.11 LINK O BHOH A 785 MN B MN P 101 1555 1555 2.68 LINK O BHOH A 800 MN B MN P 101 1555 1555 2.27 LINK N7 DG T 2 MN MN T 101 1555 1555 2.75 LINK MN MN T 101 O HOH T 201 1555 1555 2.56 LINK MN MN T 101 O HOH T 203 1555 1555 2.37 LINK OP2B DT P 5 MN B MN P 101 1555 1555 2.28 LINK MN B MN P 101 O BHOH P 216 1555 1555 2.21 CISPEP 1 GLY A 436 SER A 437 0 -2.48 SITE 1 AC1 31 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC1 31 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC1 31 GLY A 433 TRP A 434 THR A 435 GLY A 436 SITE 4 AC1 31 LYS A 438 MN A 502 MN A 503 PPV A 511 SITE 5 AC1 31 HOH A 609 HOH A 612 HOH A 619 HOH A 645 SITE 6 AC1 31 HOH A 662 HOH A 736 HOH A 785 HOH A 800 SITE 7 AC1 31 DA P 4 DT P 5 MN P 101 EDO P 102 SITE 8 AC1 31 HOH P 204 HOH P 216 DA T 5 SITE 1 AC2 7 ASP A 330 ASP A 332 TTP A 501 MN A 503 SITE 2 AC2 7 PPV A 511 HOH A 662 DT P 5 SITE 1 AC3 8 ASP A 330 ASP A 332 ASP A 418 TTP A 501 SITE 2 AC3 8 MN A 502 DA P 4 DT P 5 HOH P 204 SITE 1 AC4 5 GLU A 386 HIS A 459 HOH A 791 HOH A 840 SITE 2 AC4 5 HOH T 202 SITE 1 AC5 2 GLU A 218 HIS A 219 SITE 1 AC6 4 HIS A 208 HOH A 833 DG D 1 HOH D 118 SITE 1 AC7 6 THR A 241 ILE A 243 VAL A 246 HOH A 826 SITE 2 AC7 6 DT P 3 HOH P 214 SITE 1 AC8 5 PRO A 190 SER A 191 PRO A 192 GLN A 198 SITE 2 AC8 5 HOH A 611 SITE 1 AC9 3 CYS A 180 LYS A 438 ARG A 442 SITE 1 AD1 5 LEU A 149 LYS A 325 LEU A 326 GLN A 327 SITE 2 AD1 5 HOH A 633 SITE 1 AD2 18 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AD2 18 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AD2 18 TTP A 501 MN A 502 HOH A 609 HOH A 619 SITE 4 AD2 18 HOH A 645 HOH A 662 HOH A 736 HOH A 785 SITE 5 AD2 18 DT P 5 MN P 101 SITE 1 AD3 3 DG T 2 HOH T 201 HOH T 203 SITE 1 AD4 7 TTP A 501 PPV A 511 HOH A 609 HOH A 785 SITE 2 AD4 7 HOH A 800 DT P 5 HOH P 216 SITE 1 AD5 8 ARG A 387 GLY A 433 TRP A 434 ARG A 445 SITE 2 AD5 8 TTP A 501 DA P 4 DT P 5 HOH P 203 CRYST1 59.947 68.752 109.994 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 0.016681 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009091 0.00000