HEADER TRANSFERASE 11-FEB-23 8CIY TITLE DNA-POLYMERASE SLIDING CLAMP (DNAN) FROM ESCHERICHIA COLI IN COMPLEX TITLE 2 WITH CYCLOHEXYL-GRISELIMYCIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA SLIDING CLAMP; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA CLAMP,SLIDING CLAMP,BETA-CLAMP PROCESSIVITY FACTOR,DNA COMPND 5 POLYMERASE III BETA SLIDING CLAMP SUBUNIT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CYCLOHEXYL-GRISELIMYCIN; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DNAN, B3701, JW3678; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS DNAN, SLIDING CLAMP, DNA-POLYMERASE BETA SUBUNIT, ANTIBIOTIC, NATURAL KEYWDS 2 PRODUCT, ANTI-TUBERCULOSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.FU,Y.LIU,C.WALT,C.BADER,S.RASHEED,P.LUKAT,M.NEUBER,W.BLANKENFELDT, AUTHOR 2 O.KALININA,R.MUELLER REVDAT 2 07-FEB-24 8CIY 1 JRNL REVDAT 1 29-NOV-23 8CIY 0 JRNL AUTH C.FU,Y.LIU,C.WALT,S.RASHEED,C.D.BADER,P.LUKAT,M.NEUBER, JRNL AUTH 2 F.P.J.HAECKL,W.BLANKENFELDT,O.V.KALININA,R.MULLER JRNL TITL ELUCIDATION OF UNUSUAL BIOSYNTHESIS AND DNAN-TARGETING MODE JRNL TITL 2 OF ACTION OF POTENT ANTI-TUBERCULOSIS ANTIBIOTICS JRNL TITL 3 MYCOPLANECINS. JRNL REF NAT COMMUN V. 15 791 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38278788 JRNL DOI 10.1038/S41467-024-44953-5 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1-4487 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 67313 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.240 REMARK 3 FREE R VALUE TEST SET COUNT : 3527 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 19.9800 - 4.4800 1.00 2767 103 0.1871 0.2337 REMARK 3 2 4.4800 - 3.5700 1.00 2632 133 0.1461 0.1688 REMARK 3 3 3.5700 - 3.1200 1.00 2583 146 0.1634 0.1799 REMARK 3 4 3.1200 - 2.8300 1.00 2614 132 0.1690 0.2016 REMARK 3 5 2.8300 - 2.6300 1.00 2543 146 0.1714 0.2043 REMARK 3 6 2.6300 - 2.4800 1.00 2535 175 0.1733 0.1808 REMARK 3 7 2.4800 - 2.3500 1.00 2562 147 0.1650 0.2081 REMARK 3 8 2.3500 - 2.2500 1.00 2539 144 0.1639 0.1842 REMARK 3 9 2.2500 - 2.1600 1.00 2537 139 0.1532 0.1848 REMARK 3 10 2.1600 - 2.0900 1.00 2586 130 0.1579 0.1738 REMARK 3 11 2.0900 - 2.0200 1.00 2504 173 0.1630 0.2031 REMARK 3 12 2.0200 - 1.9700 1.00 2500 145 0.1604 0.2181 REMARK 3 13 1.9700 - 1.9100 1.00 2613 109 0.1654 0.1663 REMARK 3 14 1.9100 - 1.8700 1.00 2483 153 0.1742 0.1900 REMARK 3 15 1.8700 - 1.8200 1.00 2561 142 0.1718 0.2364 REMARK 3 16 1.8200 - 1.7900 1.00 2502 154 0.1814 0.2242 REMARK 3 17 1.7900 - 1.7500 1.00 2524 133 0.1826 0.2194 REMARK 3 18 1.7500 - 1.7200 1.00 2529 159 0.1836 0.2235 REMARK 3 19 1.7200 - 1.6900 1.00 2529 132 0.2009 0.2339 REMARK 3 20 1.6900 - 1.6600 1.00 2506 156 0.2020 0.2522 REMARK 3 21 1.6600 - 1.6300 1.00 2513 149 0.2088 0.2368 REMARK 3 22 1.6300 - 1.6100 1.00 2527 150 0.2176 0.2393 REMARK 3 23 1.6100 - 1.5800 1.00 2543 117 0.2257 0.2877 REMARK 3 24 1.5800 - 1.5600 1.00 2547 123 0.2359 0.2974 REMARK 3 25 1.5600 - 1.5400 1.00 2507 137 0.2383 0.2616 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 3201 REMARK 3 ANGLE : 0.996 4381 REMARK 3 CHIRALITY : 0.055 499 REMARK 3 PLANARITY : 0.011 586 REMARK 3 DIHEDRAL : 14.588 1272 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): -65.5375 -16.4657 20.3437 REMARK 3 T TENSOR REMARK 3 T11: 0.1323 T22: 0.1385 REMARK 3 T33: 0.1377 T12: 0.0051 REMARK 3 T13: -0.0075 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 1.0598 L22: 1.0786 REMARK 3 L33: 1.4257 L12: -0.5049 REMARK 3 L13: -0.2381 L23: 0.3618 REMARK 3 S TENSOR REMARK 3 S11: 0.0077 S12: 0.0113 S13: -0.0981 REMARK 3 S21: 0.0444 S22: 0.0162 S23: -0.0078 REMARK 3 S31: 0.0756 S32: 0.1221 S33: -0.0235 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 110 THROUGH 235 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.3638 -27.0603 17.6376 REMARK 3 T TENSOR REMARK 3 T11: 0.2008 T22: 0.1831 REMARK 3 T33: 0.2135 T12: 0.0088 REMARK 3 T13: -0.0156 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 2.8474 L22: 0.0849 REMARK 3 L33: 0.0928 L12: -0.1218 REMARK 3 L13: 0.1487 L23: 0.0789 REMARK 3 S TENSOR REMARK 3 S11: -0.0509 S12: -0.1010 S13: -0.2742 REMARK 3 S21: -0.0048 S22: 0.0266 S23: 0.0489 REMARK 3 S31: 0.0313 S32: -0.0535 S33: 0.0177 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 236 THROUGH 366 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9814 -13.3329 17.5290 REMARK 3 T TENSOR REMARK 3 T11: 0.1400 T22: 0.1567 REMARK 3 T33: 0.1549 T12: 0.0101 REMARK 3 T13: -0.0063 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 0.9296 L22: 1.0737 REMARK 3 L33: 0.5636 L12: 0.3922 REMARK 3 L13: 0.2900 L23: 0.4071 REMARK 3 S TENSOR REMARK 3 S11: 0.0392 S12: 0.0334 S13: -0.1377 REMARK 3 S21: -0.0450 S22: -0.0288 S23: -0.0245 REMARK 3 S31: 0.0440 S32: -0.0078 S33: -0.0106 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 8CIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 19.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 12.60 REMARK 200 R MERGE FOR SHELL (I) : 0.91800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.64 M CACL2 0.5 M LI ACETATE 9.4 % REMARK 280 (W/V) PEG 8000 0.1 M HEPES/NAOH 7.7 CRYOPROTECTION: 10 % (V/V) REMARK 280 (2R,3R)-2,3-BUTANEDIOL, PH 7.7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.95350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 75.36150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.95350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 75.36150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.95350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 75.36150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.95350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 75.36150 REMARK 290 SMTRY3 8 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: 9090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -215.0 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 -83.90700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 825 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 NOVEL SYNTHETIC ANALOG OF NATURAL PRODUCT GRISELIMYCIN REMARK 400 REMARK 400 THE CYCLOHEXYL-GRISELIMYCIN IS PEPTIDE-LIKE, A MEMBER OF ANTIBIOTIC REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: CYCLOHEXYL-GRISELIMYCIN 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 GLY A -2 REMARK 465 PRO A 20 REMARK 465 LEU A 21 REMARK 465 GLY A 22 REMARK 465 GLY A 23 REMARK 465 ARG A 24 REMARK 465 PRO A 25 REMARK 465 ASP A 120 REMARK 465 ASP A 121 REMARK 465 GLY A 209 REMARK 465 GLY A 210 REMARK 465 ASP A 211 REMARK 465 ASN A 212 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 LYS A 12 CG CD CE NZ REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 GLN A 123 CG CD OE1 NE2 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 534 O HOH A 607 2.07 REMARK 500 O HOH A 764 O HOH A 778 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 49 -10.38 86.97 REMARK 500 GLU A 125 -31.19 -132.71 REMARK 500 LEU A 207 58.41 -100.96 REMARK 500 THR A 341 -62.76 -121.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 137 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 896 DISTANCE = 6.06 ANGSTROMS 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 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 6 OE1 REMARK 620 2 GLU A 6 OE2 51.7 REMARK 620 3 GLY A 85 O 79.0 125.0 REMARK 620 4 GLU A 87 OE2 110.0 90.0 84.8 REMARK 620 5 HOH A 556 O 128.2 80.0 152.8 84.5 REMARK 620 6 HOH A 591 O 78.2 91.9 101.5 170.7 86.8 REMARK 620 7 HOH A 718 O 146.7 157.4 77.6 91.2 77.7 83.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 406 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 8 OE1 REMARK 620 2 GLU A 334 OE1 99.7 REMARK 620 3 GLU A 334 OE2 99.3 1.4 REMARK 620 4 HOH A 547 O 121.6 66.9 68.2 REMARK 620 5 HOH A 722 O 99.3 6.8 5.5 73.0 REMARK 620 6 HOH A 761 O 171.7 88.1 88.4 64.2 88.1 REMARK 620 7 HOH A 788 O 100.7 140.8 142.1 73.9 146.7 74.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 93 OE1 REMARK 620 2 GLU A 314 O 42.5 REMARK 620 3 GOL A 413 O1 78.0 87.2 REMARK 620 4 GOL A 413 O3 144.8 134.1 66.9 REMARK 620 5 GOL A 414 O1 145.2 124.1 136.7 69.9 REMARK 620 6 GOL A 414 O3 82.0 70.7 157.3 133.0 64.2 REMARK 620 7 HOH A 783 O 97.9 56.3 89.3 85.0 86.2 82.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 410 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 107 OG REMARK 620 2 HOH A 709 O 126.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 404 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 109 OG REMARK 620 2 GLU A 300 OE2 170.6 REMARK 620 3 HOH A 696 O 173.9 5.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 407 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 118 OD1 REMARK 620 2 HOH A 640 O 71.7 REMARK 620 3 HOH A 650 O 76.7 77.9 REMARK 620 4 HOH A 765 O 93.9 66.5 144.3 REMARK 620 5 HOH A 890 O 164.4 120.4 114.1 83.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 408 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 205 O REMARK 620 2 ASP A 208 OD1 99.5 REMARK 620 3 ASP A 208 OD2 78.1 54.2 REMARK 620 4 HOH A 501 O 92.0 54.0 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 412 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 295 O REMARK 620 2 ASN A 295 O 2.3 REMARK 620 3 ASN A 295 OD1 78.5 76.7 REMARK 620 4 HOH A 598 O 141.4 140.2 65.7 REMARK 620 5 HOH A 619 O 75.7 77.9 140.2 124.3 REMARK 620 6 HOH A 702 O 87.3 88.1 73.2 69.6 75.8 REMARK 620 7 HOH A 804 O 88.0 87.2 104.0 113.4 104.8 174.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 595 O REMARK 620 2 HOH A 735 O 130.6 REMARK 620 3 HOH A 760 O 159.2 69.3 REMARK 620 N 1 2 DBREF 8CIY A 1 366 UNP P0A988 DPO3B_ECOLI 1 366 DBREF 8CIY B 1 11 PDB 8CIY 8CIY 1 11 SEQADV 8CIY GLY A -2 UNP P0A988 EXPRESSION TAG SEQADV 8CIY GLY A -1 UNP P0A988 EXPRESSION TAG SEQADV 8CIY ARG A 0 UNP P0A988 EXPRESSION TAG SEQRES 1 A 369 GLY GLY ARG MET LYS PHE THR VAL GLU ARG GLU HIS LEU SEQRES 2 A 369 LEU LYS PRO LEU GLN GLN VAL SER GLY PRO LEU GLY GLY SEQRES 3 A 369 ARG PRO THR LEU PRO ILE LEU GLY ASN LEU LEU LEU GLN SEQRES 4 A 369 VAL ALA ASP GLY THR LEU SER LEU THR GLY THR ASP LEU SEQRES 5 A 369 GLU MET GLU MET VAL ALA ARG VAL ALA LEU VAL GLN PRO SEQRES 6 A 369 HIS GLU PRO GLY ALA THR THR VAL PRO ALA ARG LYS PHE SEQRES 7 A 369 PHE ASP ILE CYS ARG GLY LEU PRO GLU GLY ALA GLU ILE SEQRES 8 A 369 ALA VAL GLN LEU GLU GLY GLU ARG MET LEU VAL ARG SER SEQRES 9 A 369 GLY ARG SER ARG PHE SER LEU SER THR LEU PRO ALA ALA SEQRES 10 A 369 ASP PHE PRO ASN LEU ASP ASP TRP GLN SER GLU VAL GLU SEQRES 11 A 369 PHE THR LEU PRO GLN ALA THR MET LYS ARG LEU ILE GLU SEQRES 12 A 369 ALA THR GLN PHE SER MET ALA HIS GLN ASP VAL ARG TYR SEQRES 13 A 369 TYR LEU ASN GLY MET LEU PHE GLU THR GLU GLY GLU GLU SEQRES 14 A 369 LEU ARG THR VAL ALA THR ASP GLY HIS ARG LEU ALA VAL SEQRES 15 A 369 CYS SER MET PRO ILE GLY GLN SER LEU PRO SER HIS SER SEQRES 16 A 369 VAL ILE VAL PRO ARG LYS GLY VAL ILE GLU LEU MET ARG SEQRES 17 A 369 MET LEU ASP GLY GLY ASP ASN PRO LEU ARG VAL GLN ILE SEQRES 18 A 369 GLY SER ASN ASN ILE ARG ALA HIS VAL GLY ASP PHE ILE SEQRES 19 A 369 PHE THR SER LYS LEU VAL ASP GLY ARG PHE PRO ASP TYR SEQRES 20 A 369 ARG ARG VAL LEU PRO LYS ASN PRO ASP LYS HIS LEU GLU SEQRES 21 A 369 ALA GLY CYS ASP LEU LEU LYS GLN ALA PHE ALA ARG ALA SEQRES 22 A 369 ALA ILE LEU SER ASN GLU LYS PHE ARG GLY VAL ARG LEU SEQRES 23 A 369 TYR VAL SER GLU ASN GLN LEU LYS ILE THR ALA ASN ASN SEQRES 24 A 369 PRO GLU GLN GLU GLU ALA GLU GLU ILE LEU ASP VAL THR SEQRES 25 A 369 TYR SER GLY ALA GLU MET GLU ILE GLY PHE ASN VAL SER SEQRES 26 A 369 TYR VAL LEU ASP VAL LEU ASN ALA LEU LYS CYS GLU ASN SEQRES 27 A 369 VAL ARG MET MET LEU THR ASP SER VAL SER SER VAL GLN SEQRES 28 A 369 ILE GLU ASP ALA ALA SER GLN SER ALA ALA TYR VAL VAL SEQRES 29 A 369 MET PRO MET ARG LEU SEQRES 1 B 11 ACE MVA MP8 NZC LEU MP8 LEU MVA PH6 MLU GLY HET ACE B 1 6 HET MVA B 2 19 HET MP8 B 3 17 HET NZC B 4 16 HET MP8 B 6 17 HET MVA B 8 19 HET PH6 B 9 30 HET MLU B 10 22 HET CA A 401 1 HET CA A 402 1 HET CA A 403 1 HET CA A 404 1 HET CA A 405 1 HET CA A 406 1 HET MG A 407 1 HET MG A 408 1 HET MG A 409 1 HET MG A 410 1 HET MG A 411 1 HET NA A 412 1 HET GOL A 413 14 HET GOL A 414 12 HET ACT A 415 7 HETNAM ACE ACETYL GROUP HETNAM MVA N-METHYLVALINE HETNAM MP8 (4R)-4-METHYL-L-PROLINE HETNAM NZC N-METHYLIDENE-L-THREONINE HETNAM PH6 (4S)-4-CYCLOHEXYL-L-PROLINE HETNAM MLU N-METHYL-D-LEUCINE HETNAM CA CALCIUM ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL 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 PH6 C11 H19 N O2 FORMUL 2 MLU C7 H15 N O2 FORMUL 3 CA 6(CA 2+) FORMUL 9 MG 5(MG 2+) FORMUL 14 NA NA 1+ FORMUL 15 GOL 2(C3 H8 O3) FORMUL 17 ACT C2 H3 O2 1- FORMUL 18 HOH *409(H2 O) HELIX 1 AA1 ARG A 7 SER A 18 1 12 HELIX 2 AA2 LEU A 27 LEU A 30 5 4 HELIX 3 AA3 ALA A 72 LEU A 82 1 11 HELIX 4 AA4 PRO A 112 PHE A 116 5 5 HELIX 5 AA5 PRO A 131 GLN A 143 1 13 HELIX 6 AA6 PHE A 144 MET A 146 5 3 HELIX 7 AA7 ARG A 152 GLY A 157 5 6 HELIX 8 AA8 PRO A 196 LEU A 207 1 12 HELIX 9 AA9 ASP A 243 LEU A 248 1 6 HELIX 10 AB1 CYS A 260 ILE A 272 1 13 HELIX 11 AB2 VAL A 321 LYS A 332 1 12 SHEET 1 AA1 4 LYS A 2 GLU A 6 0 SHEET 2 AA1 4 GLU A 87 GLU A 93 -1 O ILE A 88 N VAL A 5 SHEET 3 AA1 4 ARG A 96 SER A 101 -1 O ARG A 100 N ALA A 89 SHEET 4 AA1 4 SER A 104 SER A 109 -1 O PHE A 106 N VAL A 99 SHEET 1 AA2 8 GLY A 66 PRO A 71 0 SHEET 2 AA2 8 ASN A 32 ALA A 38 -1 N LEU A 35 O THR A 68 SHEET 3 AA2 8 THR A 41 THR A 47 -1 O SER A 43 N GLN A 36 SHEET 4 AA2 8 MET A 51 ALA A 58 -1 O VAL A 57 N LEU A 42 SHEET 5 AA2 8 PHE A 230 LYS A 235 -1 O THR A 233 N GLU A 52 SHEET 6 AA2 8 ASN A 222 VAL A 227 -1 N ALA A 225 O PHE A 232 SHEET 7 AA2 8 LEU A 214 GLY A 219 -1 N GLY A 219 O ASN A 222 SHEET 8 AA2 8 SER A 124 LEU A 130 -1 N PHE A 128 O VAL A 216 SHEET 1 AA3 6 LYS A 254 GLY A 259 0 SHEET 2 AA3 6 ASN A 335 LEU A 340 -1 O LEU A 340 N LYS A 254 SHEET 3 AA3 6 VAL A 347 ASP A 351 -1 O GLN A 348 N MET A 339 SHEET 4 AA3 6 ALA A 357 VAL A 361 -1 O TYR A 359 N ILE A 349 SHEET 5 AA3 6 ARG A 176 VAL A 195 -1 N LEU A 177 O VAL A 360 SHEET 6 AA3 6 MET A 158 THR A 172 -1 O GLU A 165 N ILE A 184 SHEET 1 AA4 4 GLU A 301 ASP A 307 0 SHEET 2 AA4 4 GLN A 289 ASN A 295 -1 N ILE A 292 O GLU A 304 SHEET 3 AA4 4 GLY A 280 SER A 286 -1 N TYR A 284 O LYS A 291 SHEET 4 AA4 4 MET A 315 ASN A 320 -1 O ILE A 317 N LEU A 283 LINK C ACE B 1 N MVA B 2 1555 1555 1.33 LINK C MVA B 2 N MP8 B 3 1555 1555 1.34 LINK C MP8 B 3 N NZC B 4 1555 1555 1.35 LINK C NZC B 4 N LEU B 5 1555 1555 1.34 LINK OG1 NZC B 4 C GLY B 11 1555 1555 1.34 LINK C LEU B 5 N MP8 B 6 1555 1555 1.35 LINK C MP8 B 6 N LEU B 7 1555 1555 1.34 LINK C LEU B 7 N MVA B 8 1555 1555 1.34 LINK C MVA B 8 N PH6 B 9 1555 1555 1.34 LINK C PH6 B 9 N MLU B 10 1555 1555 1.35 LINK C MLU B 10 N GLY B 11 1555 1555 1.32 LINK OE1 GLU A 6 CA CA A 401 1555 1555 2.52 LINK OE2 GLU A 6 CA CA A 401 1555 1555 2.51 LINK OE1 GLU A 8 CA CA A 406 1555 1555 2.15 LINK O GLY A 85 CA CA A 401 1555 1555 2.34 LINK OE2BGLU A 87 CA CA A 401 1555 1555 2.36 LINK OE1 GLU A 93 CA CA A 403 1555 1555 2.29 LINK OG ASER A 107 MG MG A 410 1555 1555 2.87 LINK OG ASER A 109 CA CA A 404 1555 2455 2.71 LINK OD1 ASN A 118 MG MG A 407 1555 1555 2.21 LINK O ARG A 205 MG MG A 408 1555 1555 2.38 LINK OD1 ASP A 208 MG MG A 408 1555 1555 2.66 LINK OD2 ASP A 208 MG MG A 408 1555 1555 2.01 LINK O AASN A 295 NA NA A 412 1555 1555 2.41 LINK O BASN A 295 NA NA A 412 1555 1555 2.33 LINK OD1BASN A 295 NA NA A 412 1555 1555 2.79 LINK OE2 GLU A 300 CA CA A 404 1555 1555 2.81 LINK O GLU A 314 CA CA A 403 1555 1655 2.33 LINK OE1 GLU A 334 CA CA A 406 1555 3456 2.45 LINK OE2 GLU A 334 CA CA A 406 1555 3456 2.46 LINK OE1AGLN A 355 CA CA A 405 1555 1555 2.06 LINK CA CA A 401 O HOH A 556 1555 3456 2.38 LINK CA CA A 401 O HOH A 591 1555 3456 2.38 LINK CA CA A 401 O HOH A 718 1555 1555 2.37 LINK CA CA A 402 O HOH A 595 1555 1555 3.09 LINK CA CA A 402 O HOH A 735 1555 3456 3.19 LINK CA CA A 402 O HOH A 760 1555 3456 3.18 LINK CA CA A 403 O1 GOL A 413 1555 1455 2.41 LINK CA CA A 403 O3 GOL A 413 1555 1455 2.47 LINK CA CA A 403 O1 GOL A 414 1555 1555 2.39 LINK CA CA A 403 O3 GOL A 414 1555 1555 2.31 LINK CA CA A 403 O HOH A 783 1555 1555 2.40 LINK CA CA A 404 O HOH A 696 1555 2455 3.02 LINK CA CA A 406 O HOH A 547 1555 1555 2.45 LINK CA CA A 406 O HOH A 722 1555 3456 2.30 LINK CA CA A 406 O HOH A 761 1555 3456 2.43 LINK CA CA A 406 O HOH A 788 1555 3456 2.42 LINK MG MG A 407 O HOH A 640 1555 1555 2.57 LINK MG MG A 407 O HOH A 650 1555 1555 2.47 LINK MG MG A 407 O HOH A 765 1555 1555 2.43 LINK MG MG A 407 O HOH A 890 1555 1555 2.65 LINK MG MG A 408 O HOH A 501 1555 1555 2.25 LINK MG MG A 409 O HOH A 746 1555 1555 2.90 LINK MG MG A 410 O HOH A 709 1555 1555 2.91 LINK MG MG A 411 O HOH B 110 1555 1555 2.87 LINK NA NA A 412 O HOH A 598 1555 1555 2.13 LINK NA NA A 412 O HOH A 619 1555 1555 2.39 LINK NA NA A 412 O HOH A 702 1555 1555 2.65 LINK NA NA A 412 O HOH A 804 1555 1555 3.12 CISPEP 1 MVA B 8 PH6 B 9 0 -0.60 CRYST1 83.907 150.723 71.502 90.00 90.00 90.00 C 2 2 2 8 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 0.011918 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013986 0.00000