HEADER DNA BINDING PROTEIN/INHIBITOR 25-MAY-18 6DJK TITLE STRUCTURE OF DNA POLYMERASE III SUBUNIT BETA FROM RICKETTSIA TYPHI IN TITLE 2 COMPLEX WITH A NATURAL PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA SLIDING CLAMP; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SLIDING CLAMP,BETA-CLAMP PROCESSIVITY FACTOR,DNA POLYMERASE COMPND 5 III BETA SLIDING CLAMP SUBUNIT,DNA POLYMERASE III SUBUNIT BETA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RICKETTSIA TYPHI STR. WILMINGTON; SOURCE 3 ORGANISM_TAXID: 257363; SOURCE 4 STRAIN: ATCC VR-144 / WILMINGTON; SOURCE 5 GENE: DNAN, RT0405; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS SSGCID, BETA SLIDING CLAMP, DNAN, DNA POLYMERASE III SUBUNIT BETA, KEYWDS 2 GRISELMYCIN, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER KEYWDS 3 FOR INFECTIOUS DISEASE, TRANSFERASE-PEPTIDE COMPLEX, DNA BINDING KEYWDS 4 PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 3 15-NOV-23 6DJK 1 LINK REVDAT 2 11-OCT-23 6DJK 1 LINK REVDAT 1 29-MAY-19 6DJK 0 JRNL AUTH J.ABENDROTH,D.G.CONRADY,T.W.HIGGINS,D.D.LORIMER,P.S.HORANYI, JRNL AUTH 2 T.E.EDWARDS JRNL TITL STRUCTURE OF DNA POLYMERASE III SUBUNIT BETA FROM RICKETTSIA JRNL TITL 2 TYPHI IN COMPLEX WITH A NATURAL PRODUCT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3092 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 39270 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 1904 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 38.7747 - 4.4567 0.99 2767 131 0.1534 0.1707 REMARK 3 2 4.4567 - 3.5382 1.00 2706 126 0.1429 0.1574 REMARK 3 3 3.5382 - 3.0912 1.00 2663 147 0.1724 0.2232 REMARK 3 4 3.0912 - 2.8086 1.00 2698 132 0.1781 0.2303 REMARK 3 5 2.8086 - 2.6074 1.00 2629 170 0.1841 0.2502 REMARK 3 6 2.6074 - 2.4537 1.00 2656 144 0.1802 0.2048 REMARK 3 7 2.4537 - 2.3308 1.00 2651 136 0.1874 0.2623 REMARK 3 8 2.3308 - 2.2293 1.00 2690 118 0.1800 0.2128 REMARK 3 9 2.2293 - 2.1435 1.00 2620 142 0.1849 0.2162 REMARK 3 10 2.1435 - 2.0696 1.00 2617 156 0.1908 0.2451 REMARK 3 11 2.0696 - 2.0049 1.00 2674 121 0.2083 0.2570 REMARK 3 12 2.0049 - 1.9476 1.00 2671 128 0.2168 0.2564 REMARK 3 13 1.9476 - 1.8963 1.00 2649 128 0.2482 0.3228 REMARK 3 14 1.8963 - 1.8500 1.00 2675 125 0.2792 0.3082 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.92 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 'B' AND (RESID 1001 THROUGH 1011 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.2606 37.5308 39.3134 REMARK 3 T TENSOR REMARK 3 T11: 0.3361 T22: 0.5354 REMARK 3 T33: 0.3811 T12: -0.0138 REMARK 3 T13: -0.0097 T23: 0.1902 REMARK 3 L TENSOR REMARK 3 L11: 7.8086 L22: 5.9122 REMARK 3 L33: 6.1850 L12: -3.2984 REMARK 3 L13: 5.1354 L23: -0.7292 REMARK 3 S TENSOR REMARK 3 S11: -0.0418 S12: -0.1050 S13: 0.3089 REMARK 3 S21: 0.2144 S22: -0.5511 S23: -0.5559 REMARK 3 S31: -0.2515 S32: -0.4987 S33: 0.5428 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.7233 21.9348 80.5143 REMARK 3 T TENSOR REMARK 3 T11: 0.1718 T22: 0.2812 REMARK 3 T33: 0.1800 T12: 0.0138 REMARK 3 T13: -0.0054 T23: -0.0342 REMARK 3 L TENSOR REMARK 3 L11: 2.9577 L22: 3.3785 REMARK 3 L33: 4.8076 L12: 1.5295 REMARK 3 L13: 0.4181 L23: -0.9260 REMARK 3 S TENSOR REMARK 3 S11: 0.0509 S12: -0.3370 S13: 0.0637 REMARK 3 S21: 0.1050 S22: -0.1373 S23: -0.0858 REMARK 3 S31: -0.0625 S32: -0.0277 S33: 0.0854 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 230 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.4811 24.0381 52.3182 REMARK 3 T TENSOR REMARK 3 T11: 0.1722 T22: 0.1793 REMARK 3 T33: 0.1699 T12: 0.0025 REMARK 3 T13: -0.0174 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 3.6124 L22: 1.2211 REMARK 3 L33: 4.1139 L12: -0.7511 REMARK 3 L13: -1.8010 L23: 0.3839 REMARK 3 S TENSOR REMARK 3 S11: 0.0082 S12: 0.2671 S13: 0.0269 REMARK 3 S21: -0.0186 S22: -0.0762 S23: 0.0294 REMARK 3 S31: 0.0648 S32: -0.2442 S33: 0.0659 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 231 THROUGH 381 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.1033 21.1412 43.1409 REMARK 3 T TENSOR REMARK 3 T11: 0.2416 T22: 0.3983 REMARK 3 T33: 0.1913 T12: 0.0289 REMARK 3 T13: -0.0224 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 3.7550 L22: 0.8056 REMARK 3 L33: 0.9107 L12: -0.1021 REMARK 3 L13: -0.2960 L23: 0.0247 REMARK 3 S TENSOR REMARK 3 S11: 0.0130 S12: 0.7942 S13: -0.0558 REMARK 3 S21: -0.0263 S22: -0.0482 S23: -0.1204 REMARK 3 S31: 0.0456 S32: 0.1743 S33: 0.0437 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 6DJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39292 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 38.766 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.328 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.31 REMARK 200 R MERGE FOR SHELL (I) : 0.49400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.730 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: PDB ENTRY 5W7W-A AS PER MORDA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ANATRACE TOP96 SCREEN, D10: 25 % (W/V) REMARK 280 PEG 3350, 200MM LITHIUM SULFATE, 100MM BIS-TRIS: HCL, PH 6.5: REMARK 280 RIFEA.17987.A.B1.PW38224 AT 20MG/ML: SOAKED FOR 3.5H WITH 2.5MM REMARK 280 GRISELMYCIN: CRYO: 15% EG + SOAK BUFFER: TRAY 21006D10: PUCK REMARK 280 WUA6-4., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 73.75000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.86500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.75000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.86500 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: 5480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 59.92465 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 143.13419 REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY IS PEPTIDE-LIKE, A REMARK 400 MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 -7 REMARK 465 ALA A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLU A 23 REMARK 465 LYS A 24 REMARK 465 ARG A 25 REMARK 465 ASN A 26 REMARK 465 VAL A 27 REMARK 465 ILE A 28 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 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 GLN A 13 CG CD OE1 NE2 REMARK 470 VAL A 22 CG1 CG2 REMARK 470 GLU A 30 CG CD OE1 OE2 REMARK 470 MET A 50 CG SD CE REMARK 470 ASP A 93 CG OD1 OD2 REMARK 470 ILE A 94 CG1 CG2 CD1 REMARK 470 MET A 95 CG SD CE REMARK 470 LYS A 96 CG CD CE NZ REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 GLU A 150 CG CD OE1 OE2 REMARK 470 TYR A 153 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 163 CG CD CE NZ REMARK 470 LYS A 165 CG CD CE NZ REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LYS A 187 CG CD CE NZ REMARK 470 LYS A 198 CG CD CE NZ REMARK 470 LYS A 211 CG CD CE NZ REMARK 470 LYS A 254 CG CD CE NZ REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 GLU A 280 CG CD OE1 OE2 REMARK 470 LYS A 281 CG CD CE NZ REMARK 470 LYS A 292 CG CD CE NZ REMARK 470 LYS A 316 CG CD CE NZ REMARK 470 GLU A 326 CG CD OE1 OE2 REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 ILE A 356 CG1 CG2 CD1 REMARK 470 GLN A 368 CG CD OE1 NE2 REMARK 470 LYS A 380 CG CD CE NZ 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 49 -158.89 -130.49 REMARK 500 ILE A 94 43.88 -85.33 REMARK 500 ASP A 164 -130.15 60.25 REMARK 500 GLU A 215 -161.99 -112.12 REMARK 500 GLU A 232 -42.87 76.45 REMARK 500 ALA A 302 16.68 59.00 REMARK 500 MP8 B1006 49.65 -76.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues ACE B 1001 and MVA B REMARK 800 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MVA B 1002 and MP8 B REMARK 800 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues MP8 B 1003 and NZC B REMARK 800 1004 DBREF 6DJK A 1 381 UNP Q68WW0 DPO3B_RICTY 1 381 DBREF 6DJK B 1001 1011 PDB 6DJK 6DJK 1001 1011 SEQADV 6DJK MET A -7 UNP Q68WW0 INITIATING METHIONINE SEQADV 6DJK ALA A -6 UNP Q68WW0 EXPRESSION TAG SEQADV 6DJK HIS A -5 UNP Q68WW0 EXPRESSION TAG SEQADV 6DJK HIS A -4 UNP Q68WW0 EXPRESSION TAG SEQADV 6DJK HIS A -3 UNP Q68WW0 EXPRESSION TAG SEQADV 6DJK HIS A -2 UNP Q68WW0 EXPRESSION TAG SEQADV 6DJK HIS A -1 UNP Q68WW0 EXPRESSION TAG SEQADV 6DJK HIS A 0 UNP Q68WW0 EXPRESSION TAG SEQRES 1 A 389 MET ALA HIS HIS HIS HIS HIS HIS MET LEU LYS LEU ILE SEQRES 2 A 389 VAL GLU THR LYS THR LEU VAL GLN SER LEU GLY PHE ALA SEQRES 3 A 389 ARG SER VAL VAL GLU LYS ARG ASN VAL ILE PRO GLU TYR SEQRES 4 A 389 ALA ASN ILE LYS LEU SER ALA LYS ASP GLY ASN LEU GLU SEQRES 5 A 389 LEU SER SER THR ASN MET ASP LEU TYR LEU SER GLN LYS SEQRES 6 A 389 ILE ALA VAL GLN VAL LEU SER GLU GLY GLU ILE THR VAL SEQRES 7 A 389 SER THR GLN THR LEU SER ASP ILE VAL ARG LYS LEU PRO SEQRES 8 A 389 ASP SER GLU LEU THR LEU THR GLU LEU ASP ILE MET LYS SEQRES 9 A 389 LEU GLU ILE LYS GLY GLN ASN CYS GLN PHE ASN LEU PHE SEQRES 10 A 389 THR LEU PRO VAL SER SER PHE PRO ALA MET ASP SER ILE SEQRES 11 A 389 LYS PRO GLU VAL SER PHE LYS ILE SER CYS ALA ASP PHE SEQRES 12 A 389 ALA LYS ILE ILE GLU SER THR LYS PHE SER ILE SER LEU SEQRES 13 A 389 ASP GLU THR ARG TYR ASN LEU ASN GLY ILE TYR LEU HIS SEQRES 14 A 389 ILE LYS ASP LYS GLU PHE PHE ALA ALA SER THR ASP GLY SEQRES 15 A 389 HIS ARG LEU SER ILE SER TRP ILE THR LEU GLU GLU LYS SEQRES 16 A 389 ILE LYS ASN PHE GLY VAL ILE LEU PRO GLN LYS SER ALA SEQRES 17 A 389 GLU GLU ILE LEU LYS ILE VAL LYS ASP LEU LYS ASN ILE SEQRES 18 A 389 HIS GLU ASP ILE GLU ILE LEU LEU SER SER ASN LYS ILE SEQRES 19 A 389 LYS PHE ILE CYS ASN GLU ASN THR ILE LEU LEU SER LYS SEQRES 20 A 389 LEU ILE ASP GLY THR PHE PRO ASP TYR SER ALA PHE ILE SEQRES 21 A 389 PRO LYS SER SER ILE SER LYS LEU VAL ILE ASN ARG LYS SEQRES 22 A 389 ILE PHE ALA ASP SER ILE GLU ARG ILE ALA ILE ILE THR SEQRES 23 A 389 VAL GLU LYS PHE ARG ALA ILE LYS LEU SER LEU SER ARG SEQRES 24 A 389 LYS THR LEU GLU ILE SER ALA VAL GLY GLU ALA ARG GLY SEQRES 25 A 389 ASN ALA LYS GLU ILE ILE THR ALA SER GLN ASP LYS GLU SEQRES 26 A 389 SER PHE TYR GLU TYR ASN CYS ASP GLU SER LEU VAL ILE SEQRES 27 A 389 GLY PHE ASN PRO GLN TYR LEU GLU ASP VAL LEU LYS ALA SEQRES 28 A 389 VAL LYS SER ASN LEU VAL GLU LEU TYR PHE SER ASP ILE SEQRES 29 A 389 SER ALA SER ALA PRO VAL LEU ILE LYS PHE PRO GLN ASN SEQRES 30 A 389 PRO LYS ASP ILE PHE VAL ILE MET PRO VAL LYS VAL SEQRES 1 B 11 ACE MVA MP8 NZC LEU MP8 LEU MVA PRO MLU GLY HET ACE B1001 3 HET MVA B1002 8 HET MP8 B1003 8 HET NZC B1004 8 HET MP8 B1006 8 HET MVA B1008 8 HET MLU B1010 9 HET EDO A 500 4 HET EDO A 501 4 HET PEG A 502 7 HETNAM ACE ACETYL GROUP HETNAM MVA N-METHYLVALINE HETNAM MP8 (4R)-4-METHYL-L-PROLINE HETNAM NZC N-METHYLIDENE-L-THREONINE HETNAM MLU N-METHYL-D-LEUCINE HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ACE C2 H4 O FORMUL 2 MVA 2(C6 H13 N O2) FORMUL 2 MP8 2(C6 H11 N O2) FORMUL 2 NZC C5 H11 N O3 FORMUL 2 MLU C7 H15 N O2 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 PEG C4 H10 O3 FORMUL 6 HOH *245(H2 O) HELIX 1 AA1 THR A 8 VAL A 22 1 15 HELIX 2 AA2 PRO A 29 TYR A 31 5 3 HELIX 3 AA3 THR A 72 ARG A 80 1 9 HELIX 4 AA4 PRO A 112 PHE A 116 5 5 HELIX 5 AA5 CYS A 132 SER A 141 1 10 HELIX 6 AA6 THR A 142 ILE A 146 5 5 HELIX 7 AA7 ARG A 152 LEU A 155 5 4 HELIX 8 AA8 GLN A 197 ASP A 209 1 13 HELIX 9 AA9 ASP A 247 ILE A 252 5 6 HELIX 10 AB1 ARG A 264 ILE A 276 1 13 HELIX 11 AB2 ILE A 277 THR A 278 5 2 HELIX 12 AB3 VAL A 279 ARG A 283 5 5 HELIX 13 AB4 ASP A 315 SER A 318 5 4 HELIX 14 AB5 ASN A 333 VAL A 344 1 12 SHEET 1 AA1 5 GLN A 61 SER A 64 0 SHEET 2 AA1 5 LYS A 3 GLU A 7 -1 N ILE A 5 O GLN A 61 SHEET 3 AA1 5 GLU A 86 LEU A 92 -1 O LEU A 89 N LEU A 4 SHEET 4 AA1 5 LYS A 96 LYS A 100 -1 O GLU A 98 N THR A 90 SHEET 5 AA1 5 GLN A 105 PHE A 109 -1 O PHE A 106 N ILE A 99 SHEET 1 AA2 8 GLY A 66 SER A 71 0 SHEET 2 AA2 8 ASN A 33 LYS A 39 -1 N LEU A 36 O ILE A 68 SHEET 3 AA2 8 ASN A 42 THR A 48 -1 O GLU A 44 N SER A 37 SHEET 4 AA2 8 LEU A 52 ALA A 59 -1 O LEU A 54 N SER A 47 SHEET 5 AA2 8 THR A 234 LYS A 239 -1 O ILE A 235 N SER A 55 SHEET 6 AA2 8 LYS A 225 CYS A 230 -1 N CYS A 230 O THR A 234 SHEET 7 AA2 8 ASP A 216 LEU A 221 -1 N GLU A 218 O ILE A 229 SHEET 8 AA2 8 VAL A 126 SER A 131 -1 N PHE A 128 O ILE A 219 SHEET 1 AA3 9 PHE A 191 PRO A 196 0 SHEET 2 AA3 9 GLY A 157 LYS A 163 -1 N ILE A 162 O PHE A 191 SHEET 3 AA3 9 GLU A 166 THR A 172 -1 O PHE A 168 N HIS A 161 SHEET 4 AA3 9 ARG A 176 THR A 183 -1 O ILE A 182 N PHE A 167 SHEET 5 AA3 9 ASN A 369 ILE A 376 -1 O ILE A 373 N ILE A 179 SHEET 6 AA3 9 VAL A 362 PHE A 366 -1 N ILE A 364 O PHE A 374 SHEET 7 AA3 9 LEU A 348 PHE A 353 -1 N TYR A 352 O LEU A 363 SHEET 8 AA3 9 SER A 258 ASN A 263 -1 N LEU A 260 O LEU A 351 SHEET 9 AA3 9 TYR A 320 TYR A 322 -1 O GLU A 321 N VAL A 261 SHEET 1 AA4 4 GLY A 304 THR A 311 0 SHEET 2 AA4 4 THR A 293 GLY A 300 -1 N LEU A 294 O ILE A 310 SHEET 3 AA4 4 ILE A 285 LEU A 289 -1 N LYS A 286 O SER A 297 SHEET 4 AA4 4 LEU A 328 PHE A 332 -1 O LEU A 328 N LEU A 289 LINK C ACE B1001 N MVA B1002 1555 1555 1.33 LINK C MVA B1002 N MP8 B1003 1555 1555 1.33 LINK C MP8 B1003 N NZC B1004 1555 1555 1.33 LINK C NZC B1004 N LEU B1005 1555 1555 1.33 LINK OG1 NZC B1004 C GLY B1011 1555 1555 1.37 LINK C LEU B1005 N MP8 B1006 1555 1555 1.33 LINK C MP8 B1006 N LEU B1007 1555 1555 1.33 LINK C LEU B1007 N MVA B1008 1555 1555 1.33 LINK C MVA B1008 N PRO B1009 1555 1555 1.34 LINK C PRO B1009 N MLU B1010 1555 1555 1.33 LINK C MLU B1010 N GLY B1011 1555 1555 1.33 CISPEP 1 MVA B 1008 PRO B 1009 0 1.46 SITE 1 AC1 7 ASN A 49 MET A 50 ASP A 51 LEU A 52 SITE 2 AC1 7 LEU A 237 HOH A 602 HOH A 692 SITE 1 AC2 3 ILE A 252 HOH A 603 MVA B1008 SITE 1 AC3 4 ARG A 80 LYS A 81 HOH A 611 HOH A 657 SITE 1 AC4 6 HIS A 175 VAL A 379 LYS A 380 HOH A 622 SITE 2 AC4 6 MP8 B1003 HOH B1103 SITE 1 AC5 7 HIS A 175 MET A 377 PRO A 378 ACE B1001 SITE 2 AC5 7 NZC B1004 HOH B1103 HOH B1104 SITE 1 AC6 9 GLY A 174 MET A 377 PRO A 378 ACE B1001 SITE 2 AC6 9 MVA B1002 LEU B1005 GLY B1011 HOH B1104 SITE 3 AC6 9 HOH B1105 CRYST1 147.500 43.730 83.900 90.00 121.46 90.00 C 1 2 1 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 0.006780 0.000000 0.004148 0.00000 SCALE2 0.000000 0.022868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013973 0.00000