HEADER OXIDOREDUCTASE/INHIBITOR 15-MAR-15 4YRD TITLE CRYSTAL STRUCTURE OF CAPF WITH INHIBITOR 3-ISOPROPENYL-TROPOLONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSULAR POLYSACCHARIDE SYNTHESIS ENZYME CAP5F; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS (STRAIN MU50 / ATCC SOURCE 3 700699); SOURCE 4 ORGANISM_TAXID: 158878; SOURCE 5 STRAIN: MU50 / ATCC 700699; SOURCE 6 GENE: CAPF, SAV0154; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET26 KEYWDS CAPF CUPIN CAPSULAR POLYSACCHARIDE STAPHYLOCOCCUS AUREUS, KEYWDS 2 OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.NAKANO,T.CHIGIRA,T.MIYAFUSA,S.NAGATOISHI,J.M.M.CAAVEIRO,K.TSUMOTO REVDAT 4 08-NOV-23 4YRD 1 LINK REVDAT 3 05-FEB-20 4YRD 1 REMARK REVDAT 2 04-NOV-15 4YRD 1 JRNL REVDAT 1 21-OCT-15 4YRD 0 JRNL AUTH K.NAKANO,T.CHIGIRA,T.MIYAFUSA,S.NAGATOISHI,J.M.CAAVEIRO, JRNL AUTH 2 K.TSUMOTO JRNL TITL DISCOVERY AND CHARACTERIZATION OF NATURAL TROPOLONES AS JRNL TITL 2 INHIBITORS OF THE ANTIBACTERIAL TARGET CAPF FROM JRNL TITL 3 STAPHYLOCOCCUS AUREUS. JRNL REF SCI REP V. 5 15337 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 26471247 JRNL DOI 10.1038/SREP15337 REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 40164 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2139 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.50 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2761 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3130 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5560 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61000 REMARK 3 B22 (A**2) : -1.06000 REMARK 3 B33 (A**2) : 0.46000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.341 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.252 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.193 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.574 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5719 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5424 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7764 ; 1.630 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12485 ; 0.991 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 685 ; 6.338 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 276 ;39.504 ;24.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 991 ;15.208 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.347 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 876 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6410 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1304 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2746 ; 0.880 ; 1.274 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2745 ; 0.880 ; 1.274 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3426 ; 1.531 ; 1.905 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3427 ; 1.531 ; 1.905 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2973 ; 1.080 ; 1.397 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2974 ; 1.080 ; 1.397 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4338 ; 1.856 ; 2.053 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6422 ; 3.736 ;10.337 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6368 ; 3.635 ;10.262 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 356 20525 0.08 0.05 REMARK 3 2 B 1 356 20525 0.08 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 356 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0007 34.5886 -23.1554 REMARK 3 T TENSOR REMARK 3 T11: 0.1706 T22: 0.0331 REMARK 3 T33: 0.0462 T12: -0.0113 REMARK 3 T13: 0.0609 T23: -0.0217 REMARK 3 L TENSOR REMARK 3 L11: 1.2037 L22: 2.0222 REMARK 3 L33: 0.9693 L12: 1.0016 REMARK 3 L13: 0.4054 L23: 0.7055 REMARK 3 S TENSOR REMARK 3 S11: 0.1489 S12: -0.1453 S13: 0.1795 REMARK 3 S21: 0.2996 S22: -0.1133 S23: 0.0976 REMARK 3 S31: -0.0873 S32: 0.0259 S33: -0.0356 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 356 REMARK 3 ORIGIN FOR THE GROUP (A): 12.9983 6.4603 -22.8011 REMARK 3 T TENSOR REMARK 3 T11: 0.1574 T22: 0.0325 REMARK 3 T33: 0.0346 T12: -0.0097 REMARK 3 T13: -0.0542 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 1.1157 L22: 2.0184 REMARK 3 L33: 1.0225 L12: 0.8806 REMARK 3 L13: -0.5351 L23: -0.8183 REMARK 3 S TENSOR REMARK 3 S11: 0.1103 S12: -0.1021 S13: -0.1288 REMARK 3 S21: 0.2847 S22: -0.0938 S23: -0.0658 REMARK 3 S31: 0.0703 S32: -0.0351 S33: -0.0165 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4YRD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42336 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 52.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3ST7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE 100MM, POTASSIUM REMARK 280 PHOSPHATE 200MM, PEG 3350 18%, PH 7.2, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 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+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 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 79.18000 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 79.18000 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 39.29000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 97.31000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 97.31000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.18000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 97.31000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 79.18000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.29000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 97.31000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLN A 96 REMARK 465 ALA A 97 REMARK 465 THR A 98 REMARK 465 GLN A 99 REMARK 465 ASP A 100 REMARK 465 ASN A 101 REMARK 465 PRO A 102 REMARK 465 TYR A 103 REMARK 465 GLY A 104 REMARK 465 GLU A 105 REMARK 465 SER A 106 REMARK 465 LYS A 107 REMARK 465 LEU A 108 REMARK 465 GLN A 109 REMARK 465 GLY A 110 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 GLN B 96 REMARK 465 ALA B 97 REMARK 465 THR B 98 REMARK 465 GLN B 99 REMARK 465 ASP B 100 REMARK 465 ASN B 101 REMARK 465 PRO B 102 REMARK 465 TYR B 103 REMARK 465 GLY B 104 REMARK 465 GLU B 105 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 ASP A 344 CB ASP A 344 CG -0.126 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 ARG A 222 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 344 CB - CG - OD1 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG B 307 NE - CZ - NH2 ANGL. DEV. = -3.3 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 PRO A 131 -163.95 -78.28 REMARK 500 TYR A 142 -110.11 -140.13 REMARK 500 THR A 292 -35.23 -133.88 REMARK 500 LEU A 367 118.88 -160.46 REMARK 500 LYS B 86 74.26 -105.85 REMARK 500 PRO B 131 -163.53 -79.05 REMARK 500 TYR B 142 -106.79 -136.64 REMARK 500 THR B 292 -35.91 -133.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 288 NE2 REMARK 620 2 GLU A 295 OE1 137.9 REMARK 620 3 HIS A 337 NE2 106.5 97.7 REMARK 620 4 3IT A 402 OAC 96.4 117.1 91.6 REMARK 620 5 3IT A 402 OAD 79.3 87.3 163.3 72.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 288 NE2 REMARK 620 2 GLU B 295 OE2 144.8 REMARK 620 3 HIS B 337 NE2 108.9 90.1 REMARK 620 4 3IT B 402 OAC 98.4 111.3 90.0 REMARK 620 5 3IT B 402 OAD 77.2 93.0 163.2 73.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3IT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3IT B 402 DBREF 4YRD A 1 369 UNP Q99X63 Q99X63_STAAM 1 369 DBREF 4YRD B 1 369 UNP Q99X63 Q99X63_STAAM 1 369 SEQADV 4YRD GLY A -2 UNP Q99X63 EXPRESSION TAG SEQADV 4YRD GLY A -1 UNP Q99X63 EXPRESSION TAG SEQADV 4YRD SER A 0 UNP Q99X63 EXPRESSION TAG SEQADV 4YRD GLY A 57 UNP Q99X63 ASN 57 ENGINEERED MUTATION SEQADV 4YRD A UNP Q99X63 ARG 58 DELETION SEQADV 4YRD A UNP Q99X63 PRO 59 DELETION SEQADV 4YRD A UNP Q99X63 GLU 60 DELETION SEQADV 4YRD A UNP Q99X63 HIS 61 DELETION SEQADV 4YRD A UNP Q99X63 ASP 62 DELETION SEQADV 4YRD A UNP Q99X63 LYS 63 DELETION SEQADV 4YRD A UNP Q99X63 GLU 64 DELETION SEQADV 4YRD A UNP Q99X63 PHE 65 DELETION SEQADV 4YRD A UNP Q99X63 SER 66 DELETION SEQADV 4YRD A UNP Q99X63 LEU 67 DELETION SEQADV 4YRD A UNP Q99X63 GLY 68 DELETION SEQADV 4YRD A UNP Q99X63 ASN 69 DELETION SEQADV 4YRD A UNP Q99X63 VAL 70 DELETION SEQADV 4YRD GLY B -2 UNP Q99X63 EXPRESSION TAG SEQADV 4YRD GLY B -1 UNP Q99X63 EXPRESSION TAG SEQADV 4YRD SER B 0 UNP Q99X63 EXPRESSION TAG SEQADV 4YRD GLY B 57 UNP Q99X63 ASN 57 ENGINEERED MUTATION SEQADV 4YRD B UNP Q99X63 ARG 58 DELETION SEQADV 4YRD B UNP Q99X63 PRO 59 DELETION SEQADV 4YRD B UNP Q99X63 GLU 60 DELETION SEQADV 4YRD B UNP Q99X63 HIS 61 DELETION SEQADV 4YRD B UNP Q99X63 ASP 62 DELETION SEQADV 4YRD B UNP Q99X63 LYS 63 DELETION SEQADV 4YRD B UNP Q99X63 GLU 64 DELETION SEQADV 4YRD B UNP Q99X63 PHE 65 DELETION SEQADV 4YRD B UNP Q99X63 SER 66 DELETION SEQADV 4YRD B UNP Q99X63 LEU 67 DELETION SEQADV 4YRD B UNP Q99X63 GLY 68 DELETION SEQADV 4YRD B UNP Q99X63 ASN 69 DELETION SEQADV 4YRD B UNP Q99X63 VAL 70 DELETION SEQRES 1 A 359 GLY GLY SER MET ASN ILE VAL ILE THR GLY ALA LYS GLY SEQRES 2 A 359 PHE VAL GLY LYS ASN LEU LYS ALA ASP LEU THR SER THR SEQRES 3 A 359 THR ASP HIS HIS ILE PHE GLU VAL HIS ARG GLN THR LYS SEQRES 4 A 359 GLU GLU GLU LEU GLU SER ALA LEU LEU LYS ALA ASP PHE SEQRES 5 A 359 ILE VAL HIS LEU ALA GLY VAL GLY SER TYR LEU ASP HIS SEQRES 6 A 359 VAL LEU ASP ILE LEU THR ARG ASN THR LYS LYS PRO ALA SEQRES 7 A 359 ILE LEU LEU SER SER SER ILE GLN ALA THR GLN ASP ASN SEQRES 8 A 359 PRO TYR GLY GLU SER LYS LEU GLN GLY GLU GLN LEU LEU SEQRES 9 A 359 ARG GLU TYR ALA GLU GLU TYR GLY ASN THR VAL TYR ILE SEQRES 10 A 359 TYR ARG TRP PRO ASN LEU PHE GLY LYS TRP CYS LYS PRO SEQRES 11 A 359 ASN TYR ASN SER VAL ILE ALA THR PHE CYS TYR LYS ILE SEQRES 12 A 359 ALA ARG ASN GLU GLU ILE GLN VAL ASN ASP ARG ASN VAL SEQRES 13 A 359 GLU LEU THR LEU ASN TYR VAL ASP ASP ILE VAL ALA GLU SEQRES 14 A 359 ILE LYS ARG ALA ILE GLU GLY THR PRO THR ILE GLU ASN SEQRES 15 A 359 GLY VAL PRO THR VAL PRO ASN VAL PHE LYS VAL THR LEU SEQRES 16 A 359 GLY GLU ILE VAL ASP LEU LEU TYR LYS PHE LYS GLN SER SEQRES 17 A 359 ARG LEU ASP ARG THR LEU PRO LYS LEU ASP ASN LEU PHE SEQRES 18 A 359 GLU LYS ASP LEU TYR SER THR TYR LEU SER TYR LEU PRO SEQRES 19 A 359 SER THR ASP PHE SER TYR PRO LEU LEU MET ASN VAL ASP SEQRES 20 A 359 ASP ARG GLY SER PHE THR GLU PHE ILE LYS THR PRO ASP SEQRES 21 A 359 ARG GLY GLN VAL SER VAL ASN ILE SER LYS PRO GLY ILE SEQRES 22 A 359 THR LYS GLY ASN HIS TRP HIS HIS THR LYS ASN GLU LYS SEQRES 23 A 359 PHE LEU VAL VAL SER GLY LYS GLY VAL ILE ARG PHE ARG SEQRES 24 A 359 HIS VAL ASN ASP ASP GLU ILE ILE GLU TYR TYR VAL SER SEQRES 25 A 359 GLY ASP LYS LEU GLU VAL VAL ASP ILE PRO VAL GLY TYR SEQRES 26 A 359 THR HIS ASN ILE GLU ASN LEU GLY ASP THR ASP MET VAL SEQRES 27 A 359 THR ILE MET TRP VAL ASN GLU MET PHE ASP PRO ASN GLN SEQRES 28 A 359 PRO ASP THR TYR PHE LEU GLU VAL SEQRES 1 B 359 GLY GLY SER MET ASN ILE VAL ILE THR GLY ALA LYS GLY SEQRES 2 B 359 PHE VAL GLY LYS ASN LEU LYS ALA ASP LEU THR SER THR SEQRES 3 B 359 THR ASP HIS HIS ILE PHE GLU VAL HIS ARG GLN THR LYS SEQRES 4 B 359 GLU GLU GLU LEU GLU SER ALA LEU LEU LYS ALA ASP PHE SEQRES 5 B 359 ILE VAL HIS LEU ALA GLY VAL GLY SER TYR LEU ASP HIS SEQRES 6 B 359 VAL LEU ASP ILE LEU THR ARG ASN THR LYS LYS PRO ALA SEQRES 7 B 359 ILE LEU LEU SER SER SER ILE GLN ALA THR GLN ASP ASN SEQRES 8 B 359 PRO TYR GLY GLU SER LYS LEU GLN GLY GLU GLN LEU LEU SEQRES 9 B 359 ARG GLU TYR ALA GLU GLU TYR GLY ASN THR VAL TYR ILE SEQRES 10 B 359 TYR ARG TRP PRO ASN LEU PHE GLY LYS TRP CYS LYS PRO SEQRES 11 B 359 ASN TYR ASN SER VAL ILE ALA THR PHE CYS TYR LYS ILE SEQRES 12 B 359 ALA ARG ASN GLU GLU ILE GLN VAL ASN ASP ARG ASN VAL SEQRES 13 B 359 GLU LEU THR LEU ASN TYR VAL ASP ASP ILE VAL ALA GLU SEQRES 14 B 359 ILE LYS ARG ALA ILE GLU GLY THR PRO THR ILE GLU ASN SEQRES 15 B 359 GLY VAL PRO THR VAL PRO ASN VAL PHE LYS VAL THR LEU SEQRES 16 B 359 GLY GLU ILE VAL ASP LEU LEU TYR LYS PHE LYS GLN SER SEQRES 17 B 359 ARG LEU ASP ARG THR LEU PRO LYS LEU ASP ASN LEU PHE SEQRES 18 B 359 GLU LYS ASP LEU TYR SER THR TYR LEU SER TYR LEU PRO SEQRES 19 B 359 SER THR ASP PHE SER TYR PRO LEU LEU MET ASN VAL ASP SEQRES 20 B 359 ASP ARG GLY SER PHE THR GLU PHE ILE LYS THR PRO ASP SEQRES 21 B 359 ARG GLY GLN VAL SER VAL ASN ILE SER LYS PRO GLY ILE SEQRES 22 B 359 THR LYS GLY ASN HIS TRP HIS HIS THR LYS ASN GLU LYS SEQRES 23 B 359 PHE LEU VAL VAL SER GLY LYS GLY VAL ILE ARG PHE ARG SEQRES 24 B 359 HIS VAL ASN ASP ASP GLU ILE ILE GLU TYR TYR VAL SER SEQRES 25 B 359 GLY ASP LYS LEU GLU VAL VAL ASP ILE PRO VAL GLY TYR SEQRES 26 B 359 THR HIS ASN ILE GLU ASN LEU GLY ASP THR ASP MET VAL SEQRES 27 B 359 THR ILE MET TRP VAL ASN GLU MET PHE ASP PRO ASN GLN SEQRES 28 B 359 PRO ASP THR TYR PHE LEU GLU VAL HET ZN A 401 1 HET 3IT A 402 12 HET ZN B 401 1 HET 3IT B 402 12 HETNAM ZN ZINC ION HETNAM 3IT 2-HYDROXY-3-(PROP-1-EN-2-YL)CYCLOHEPTA-2,4,6-TRIEN-1- HETNAM 2 3IT ONE HETSYN 3IT 3-ISOPROPENYL-TROPOLONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 3IT 2(C10 H10 O2) FORMUL 7 HOH *194(H2 O) HELIX 1 AA1 GLY A 10 THR A 24 1 15 HELIX 2 AA2 LYS A 36 ALA A 47 1 12 HELIX 3 AA3 GLY A 57 THR A 81 1 12 HELIX 4 AA4 GLN A 112 GLY A 122 1 11 HELIX 5 AA5 SER A 144 ARG A 155 1 12 HELIX 6 AA6 VAL A 173 GLU A 185 1 13 HELIX 7 AA7 LEU A 205 ARG A 222 1 18 HELIX 8 AA8 ASN A 229 SER A 241 1 13 HELIX 9 AA9 TYR A 242 LEU A 243 5 2 HELIX 10 AB1 PRO A 244 ASP A 247 5 4 HELIX 11 AB2 GLY B 10 THR B 24 1 15 HELIX 12 AB3 LYS B 36 ALA B 47 1 12 HELIX 13 AB4 GLY B 57 THR B 81 1 12 HELIX 14 AB5 GLY B 110 GLY B 122 1 13 HELIX 15 AB6 SER B 144 ARG B 155 1 12 HELIX 16 AB7 VAL B 173 GLU B 185 1 13 HELIX 17 AB8 LEU B 205 ARG B 222 1 18 HELIX 18 AB9 ASN B 229 TYR B 242 1 14 HELIX 19 AC1 LEU B 243 ASP B 247 5 5 SHEET 1 AA1 5 HIS A 27 GLU A 30 0 SHEET 2 AA1 5 ASN A 2 THR A 6 1 N ILE A 3 O PHE A 29 SHEET 3 AA1 5 PHE A 49 HIS A 52 1 O VAL A 51 N VAL A 4 SHEET 4 AA1 5 ALA A 88 SER A 92 1 O LEU A 90 N ILE A 50 SHEET 5 AA1 5 VAL A 125 TYR A 128 1 O TYR A 126 N ILE A 89 SHEET 1 AA2 3 ASN A 132 PHE A 134 0 SHEET 2 AA2 3 GLU A 167 TYR A 172 1 O ASN A 171 N PHE A 134 SHEET 3 AA2 3 PHE A 201 THR A 204 -1 O VAL A 203 N LEU A 168 SHEET 1 AA3 7 SER A 249 PRO A 251 0 SHEET 2 AA3 7 GLU B 327 ILE B 331 -1 O VAL B 328 N TYR A 250 SHEET 3 AA3 7 GLU B 295 SER B 301 -1 N PHE B 297 O VAL B 329 SHEET 4 AA3 7 MET B 347 VAL B 353 -1 O VAL B 348 N SER B 301 SHEET 5 AA3 7 GLN B 273 SER B 279 -1 N ASN B 277 O THR B 349 SHEET 6 AA3 7 GLY B 260 LYS B 267 -1 N THR B 263 O VAL B 276 SHEET 7 AA3 7 ASN B 255 ASP B 257 -1 N ASP B 257 O GLY B 260 SHEET 1 AA4 7 ASN A 255 ASP A 257 0 SHEET 2 AA4 7 GLY A 260 LYS A 267 -1 O GLY A 260 N ASP A 257 SHEET 3 AA4 7 GLN A 273 SER A 279 -1 O VAL A 276 N THR A 263 SHEET 4 AA4 7 MET A 347 VAL A 353 -1 O THR A 349 N ASN A 277 SHEET 5 AA4 7 GLU A 295 SER A 301 -1 N SER A 301 O VAL A 348 SHEET 6 AA4 7 GLU A 327 ILE A 331 -1 O VAL A 329 N PHE A 297 SHEET 7 AA4 7 SER B 249 PRO B 251 -1 O TYR B 250 N VAL A 328 SHEET 1 AA5 5 ILE A 316 SER A 322 0 SHEET 2 AA5 5 LYS A 303 HIS A 310 -1 N PHE A 308 O ILE A 317 SHEET 3 AA5 5 TYR A 335 ASN A 341 -1 O THR A 336 N ARG A 309 SHEET 4 AA5 5 THR A 284 TRP A 289 -1 N LYS A 285 O ILE A 339 SHEET 5 AA5 5 TYR A 365 PHE A 366 -1 O TYR A 365 N TRP A 289 SHEET 1 AA6 5 HIS B 27 GLU B 30 0 SHEET 2 AA6 5 ASN B 2 THR B 6 1 N ILE B 3 O HIS B 27 SHEET 3 AA6 5 PHE B 49 HIS B 52 1 O VAL B 51 N VAL B 4 SHEET 4 AA6 5 ALA B 88 SER B 92 1 O LEU B 90 N ILE B 50 SHEET 5 AA6 5 VAL B 125 TYR B 128 1 O TYR B 126 N ILE B 89 SHEET 1 AA7 3 ASN B 132 PHE B 134 0 SHEET 2 AA7 3 GLU B 167 TYR B 172 1 O ASN B 171 N PHE B 134 SHEET 3 AA7 3 PHE B 201 THR B 204 -1 O VAL B 203 N LEU B 168 SHEET 1 AA8 5 ILE B 316 SER B 322 0 SHEET 2 AA8 5 LYS B 303 HIS B 310 -1 N PHE B 308 O ILE B 317 SHEET 3 AA8 5 TYR B 335 ASN B 341 -1 O THR B 336 N ARG B 309 SHEET 4 AA8 5 THR B 284 TRP B 289 -1 N LYS B 285 O ILE B 339 SHEET 5 AA8 5 TYR B 365 PHE B 366 -1 O TYR B 365 N TRP B 289 LINK NE2 HIS A 288 ZN ZN A 401 1555 1555 2.40 LINK OE1 GLU A 295 ZN ZN A 401 1555 1555 2.31 LINK NE2 HIS A 337 ZN ZN A 401 1555 1555 2.48 LINK ZN ZN A 401 OAC 3IT A 402 1555 1555 2.22 LINK ZN ZN A 401 OAD 3IT A 402 1555 1555 1.87 LINK NE2 HIS B 288 ZN ZN B 401 1555 1555 2.36 LINK OE2 GLU B 295 ZN ZN B 401 1555 1555 2.50 LINK NE2 HIS B 337 ZN ZN B 401 1555 1555 2.45 LINK ZN ZN B 401 OAC 3IT B 402 1555 1555 2.21 LINK ZN ZN B 401 OAD 3IT B 402 1555 1555 1.86 SITE 1 AC1 4 HIS A 288 GLU A 295 HIS A 337 3IT A 402 SITE 1 AC2 7 PHE A 262 HIS A 288 GLU A 295 PHE A 297 SITE 2 AC2 7 HIS A 337 MET A 351 ZN A 401 SITE 1 AC3 4 HIS B 288 GLU B 295 HIS B 337 3IT B 402 SITE 1 AC4 7 PHE B 262 HIS B 288 GLU B 295 PHE B 297 SITE 2 AC4 7 HIS B 337 MET B 351 ZN B 401 CRYST1 78.580 194.620 158.360 90.00 90.00 90.00 C 2 2 21 16 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 0.012726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005138 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006315 0.00000