HEADER TRANSFERASE/DNA 21-NOV-16 5TYU TITLE DNA POLYMERASE MU REACTANT COMPLEX, MN2+ (4 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 5TYU 1 LINK REVDAT 3 18-DEC-19 5TYU 1 REMARK REVDAT 2 27-SEP-17 5TYU 1 REMARK REVDAT 1 30-AUG-17 5TYU 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. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 28577 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1433 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 33.3701 - 4.4088 1.00 2905 156 0.1819 0.2094 REMARK 3 2 4.4088 - 3.5006 1.00 2764 139 0.1574 0.1731 REMARK 3 3 3.5006 - 3.0584 1.00 2767 140 0.1798 0.1920 REMARK 3 4 3.0584 - 2.7789 1.00 2711 156 0.2010 0.2279 REMARK 3 5 2.7789 - 2.5798 1.00 2692 142 0.2011 0.2561 REMARK 3 6 2.5798 - 2.4278 1.00 2719 134 0.1943 0.2389 REMARK 3 7 2.4278 - 2.3062 1.00 2662 160 0.1967 0.2285 REMARK 3 8 2.3062 - 2.2059 1.00 2711 130 0.2120 0.2378 REMARK 3 9 2.2059 - 2.1210 1.00 2668 151 0.2236 0.2479 REMARK 3 10 2.1210 - 2.0478 0.95 2545 125 0.2423 0.2673 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.33 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 3237 REMARK 3 ANGLE : 0.571 4492 REMARK 3 CHIRALITY : 0.044 489 REMARK 3 PLANARITY : 0.003 522 REMARK 3 DIHEDRAL : 12.393 1030 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 5TYU 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_1000225051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-16 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-BM 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28596 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.85700 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 (%): 53.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 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 30.07750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.29400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.11150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.29400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.07750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.11150 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: 6800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 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 GLU A 207 CD OE1 OE2 REMARK 470 LYS A 249 CE NZ 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 CD OE1 NE2 REMARK 470 GLN A 300 CD OE1 NE2 REMARK 470 GLU A 304 CG CD OE1 OE2 REMARK 470 LYS A 339 CD CE NZ REMARK 470 GLN A 355 CD OE1 NE2 REMARK 470 GLN A 357 CD OE1 NE2 REMARK 470 GLN A 466 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 645 O HOH A 784 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 -0.125 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 GLN A 268 71.06 -113.60 REMARK 500 LEU A 310 106.03 -162.39 REMARK 500 THR A 318 -152.66 -131.46 REMARK 500 THR A 318 -152.74 -127.13 REMARK 500 PRO A 397 108.40 -51.59 REMARK 500 PRO A 397 109.38 -50.74 REMARK 500 SER A 411 -152.10 -164.40 REMARK 500 ASN A 493 46.84 -87.08 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 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 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 241 O REMARK 620 2 ILE A 243 O 96.6 REMARK 620 3 VAL A 246 O 86.4 94.2 REMARK 620 4 HOH A 773 O 88.0 93.7 170.8 REMARK 620 5 DT P 3 OP1 171.7 91.4 90.8 93.8 REMARK 620 6 HOH P 203 O 93.7 168.0 80.2 92.9 78.1 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 OD2 REMARK 620 2 ASP A 332 OD1 109.6 REMARK 620 3 ASP A 418 OD2 91.1 94.2 REMARK 620 4 DA P 4 O3' 151.1 98.2 94.5 REMARK 620 5 DT P 5 OP1 102.5 93.2 161.3 67.4 REMARK 620 6 HOH P 202 O 78.2 169.6 92.4 73.2 78.2 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 OD1 REMARK 620 2 ASP A 332 OD2 95.8 REMARK 620 3 TTP A 501 O2A 96.7 93.9 REMARK 620 4 TTP A 501 O1B 171.9 92.3 81.8 REMARK 620 5 TTP A 501 O2G 86.5 176.6 88.3 85.5 REMARK 620 6 PPV A 507 O21 165.0 95.9 91.8 11.0 81.4 REMARK 620 7 PPV A 507 O32 85.1 178.4 87.3 86.9 1.8 83.0 REMARK 620 8 HOH A 718 O 90.8 88.2 171.9 90.4 89.3 80.2 90.5 REMARK 620 9 DT P 5 OP1 87.5 83.1 15.0 92.6 99.5 103.3 98.2 170.9 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 506 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 330 OD2 REMARK 620 2 ASP A 332 OD1 109.6 REMARK 620 3 ASP A 418 OD2 91.1 94.2 REMARK 620 4 TTP A 501 O2A 93.5 89.9 172.4 REMARK 620 5 DA P 4 O3' 161.4 88.9 86.0 87.7 REMARK 620 6 HOH P 202 O 78.2 169.6 92.4 82.7 83.5 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 507 O31 REMARK 620 2 DT P 5 OP2 101.2 REMARK 620 3 HOH P 212 O 105.5 86.1 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 NA A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTT 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 EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 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: 5TYV 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 5TYU A 132 494 UNP Q9NP87 DPOLM_HUMAN 132 494 DBREF 5TYU T 1 9 PDB 5TYU 5TYU 1 9 DBREF 5TYU P 1 5 PDB 5TYU 5TYU 1 5 DBREF 5TYU D 1 4 PDB 5TYU 5TYU 1 4 SEQADV 5TYU GLY A 127 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYU SER A 128 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYU ALA A 129 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYU ALA A 130 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYU ALA A 131 UNP Q9NP87 EXPRESSION TAG SEQADV 5TYU A UNP Q9NP87 PRO 398 DELETION SEQADV 5TYU A UNP Q9NP87 GLY 399 DELETION SEQADV 5TYU A UNP Q9NP87 ALA 400 DELETION SEQADV 5TYU A UNP Q9NP87 ALA 401 DELETION SEQADV 5TYU A UNP Q9NP87 VAL 402 DELETION SEQADV 5TYU A UNP Q9NP87 GLY 403 DELETION SEQADV 5TYU A UNP Q9NP87 GLY 404 DELETION SEQADV 5TYU A UNP Q9NP87 SER 405 DELETION SEQADV 5TYU A UNP Q9NP87 THR 406 DELETION SEQADV 5TYU A UNP Q9NP87 ARG 407 DELETION SEQADV 5TYU A UNP Q9NP87 PRO 408 DELETION SEQADV 5TYU A UNP Q9NP87 CYS 409 DELETION SEQADV 5TYU 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 NA A 505 1 HET CA A 506 1 HET PPV A 507 9 HET DTT A 508 1 HET EDO A 509 4 HET EDO A 510 4 HET EPE A 511 5 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 CA CALCIUM ION HETNAM PPV PYROPHOSPHATE HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN DTT 1,4-DITHIOTHREITOL HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 5 TTP C10 H17 N2 O14 P3 FORMUL 6 MN 4(MN 2+) FORMUL 9 NA NA 1+ FORMUL 10 CA CA 2+ FORMUL 11 PPV H4 O7 P2 FORMUL 12 DTT C4 H10 O2 S2 FORMUL 13 EDO 3(C2 H6 O2) FORMUL 15 EPE C8 H18 N2 O4 S FORMUL 18 HOH *248(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 GLN A 268 1 8 HELIX 10 AB1 PRO A 269 LEU A 272 5 4 HELIX 11 AB2 THR A 273 HIS A 282 1 10 HELIX 12 AB3 HIS A 282 SER A 287 1 6 HELIX 13 AB4 ARG A 292 LEU A 310 1 19 HELIX 14 AB5 THR A 318 ARG A 323 1 6 HELIX 15 AB6 GLY A 345 GLN A 357 1 13 HELIX 16 AB7 PRO A 423 SER A 425 5 3 HELIX 17 AB8 GLN A 426 GLY A 436 1 11 HELIX 18 AB9 SER A 437 GLY A 453 1 17 HELIX 19 AC1 SER A 474 LEU A 482 1 9 HELIX 20 AC2 PRO A 488 ARG A 492 5 5 SHEET 1 AA1 2 VAL A 290 LEU A 291 0 SHEET 2 AA1 2 GLN A 327 GLY A 328 -1 O GLY A 328 N VAL A 290 SHEET 1 AA2 5 THR A 314 LEU A 317 0 SHEET 2 AA2 5 ASP A 330 THR A 336 -1 O LEU A 334 N THR A 316 SHEET 3 AA2 5 SER A 411 VAL A 421 1 O VAL A 420 N ILE A 335 SHEET 4 AA2 5 ARG A 387 GLN A 396 -1 N PHE A 392 O VAL A 415 SHEET 5 AA2 5 ILE A 360 TYR A 362 -1 N LEU A 361 O ILE A 391 SHEET 1 AA3 3 TRP A 455 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 508 1555 1555 2.05 LINK NE2 HIS A 219 MN MN A 504 1555 1555 2.23 LINK O THR A 241 NA NA A 505 1555 1555 2.44 LINK O ILE A 243 NA NA A 505 1555 1555 2.30 LINK O VAL A 246 NA NA A 505 1555 1555 2.36 LINK OD2 ASP A 330 MN B MN A 502 1555 1555 1.92 LINK OD1 ASP A 330 MN MN A 503 1555 1555 2.12 LINK OD2 ASP A 330 CA A CA A 506 1555 1555 1.92 LINK OD1 ASP A 332 MN B MN A 502 1555 1555 2.13 LINK OD2 ASP A 332 MN MN A 503 1555 1555 2.22 LINK OD1 ASP A 332 CA A CA A 506 1555 1555 2.13 LINK OD2 ASP A 418 MN B MN A 502 1555 1555 1.99 LINK OD2 ASP A 418 CA A CA A 506 1555 1555 1.99 LINK O2AATTP A 501 MN MN A 503 1555 1555 1.79 LINK O1BATTP A 501 MN MN A 503 1555 1555 2.14 LINK O2GATTP A 501 MN MN A 503 1555 1555 2.08 LINK O2AATTP A 501 CA A CA A 506 1555 1555 2.72 LINK MN B MN A 502 O3'B DA P 4 1555 1555 2.42 LINK MN B MN A 502 OP1B DT P 5 1555 1555 2.03 LINK MN B MN A 502 O HOH P 202 1555 1555 2.55 LINK MN MN A 503 O21BPPV A 507 1555 1555 2.31 LINK MN MN A 503 O32BPPV A 507 1555 1555 2.25 LINK MN MN A 503 O HOH A 718 1555 1555 2.13 LINK MN MN A 503 OP1B DT P 5 1555 1555 2.42 LINK NA NA A 505 O HOH A 773 1555 1555 2.37 LINK NA NA A 505 OP1 DT P 3 1555 1555 2.54 LINK NA NA A 505 O HOH P 203 1555 1555 2.68 LINK CA A CA A 506 O3'A DA P 4 1555 1555 2.50 LINK CA A CA A 506 O HOH P 202 1555 1555 2.55 LINK O31BPPV A 507 MN B MN P 101 1555 1555 2.44 LINK OP2B DT P 5 MN B MN P 101 1555 1555 1.91 LINK MN B MN P 101 O BHOH P 212 1555 1555 2.50 CISPEP 1 GLY A 436 SER A 437 0 -4.01 SITE 1 AC1 30 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC1 30 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC1 30 GLY A 433 TRP A 434 THR A 435 GLY A 436 SITE 4 AC1 30 LYS A 438 MN A 502 MN A 503 CA A 506 SITE 5 AC1 30 PPV A 507 HOH A 611 HOH A 625 HOH A 664 SITE 6 AC1 30 HOH A 677 HOH A 696 HOH A 718 DA P 4 SITE 7 AC1 30 DT P 5 MN P 101 EDO P 102 HOH P 202 SITE 8 AC1 30 HOH P 212 DA T 5 SITE 1 AC2 8 ASP A 330 ASP A 332 ASP A 418 TTP A 501 SITE 2 AC2 8 MN A 503 DA P 4 DT P 5 HOH P 202 SITE 1 AC3 8 ASP A 330 ASP A 332 TTP A 501 MN A 502 SITE 2 AC3 8 CA A 506 PPV A 507 HOH A 718 DT P 5 SITE 1 AC4 2 GLU A 218 HIS A 219 SITE 1 AC5 6 THR A 241 ILE A 243 VAL A 246 HOH A 773 SITE 2 AC5 6 DT P 3 HOH P 203 SITE 1 AC6 8 ASP A 330 ASP A 332 ASP A 418 TTP A 501 SITE 2 AC6 8 MN A 503 DA P 4 DT P 5 HOH P 202 SITE 1 AC7 18 GLY A 319 GLY A 320 ARG A 323 LYS A 325 SITE 2 AC7 18 GLY A 328 HIS A 329 ASP A 330 ASP A 332 SITE 3 AC7 18 TTP A 501 MN A 503 HOH A 611 HOH A 625 SITE 4 AC7 18 HOH A 664 HOH A 677 HOH A 696 HOH A 718 SITE 5 AC7 18 DT P 5 MN P 101 SITE 1 AC8 2 CYS A 180 HOH A 760 SITE 1 AC9 7 ARG A 253 ARG A 256 GLU A 451 LYS A 452 SITE 2 AC9 7 GLY A 453 HOH A 619 HOH A 673 SITE 1 AD1 4 HIS A 152 THR A 314 THR A 336 HOH A 667 SITE 1 AD2 5 LEU A 149 LYS A 325 LEU A 326 GLN A 327 SITE 2 AD2 5 HOH A 710 SITE 1 AD3 5 HIS A 329 TTP A 501 PPV A 507 DT P 5 SITE 2 AD3 5 HOH P 212 SITE 1 AD4 7 ARG A 387 GLY A 433 TRP A 434 ARG A 445 SITE 2 AD4 7 TTP A 501 DA P 4 DT P 5 CRYST1 60.155 62.223 118.588 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 0.016624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016071 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008433 0.00000