HEADER LIGASE/LIGASE INHIBITOR 23-DEC-11 3V8L TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS BIOTIN PROTEIN LIGASE IN TITLE 2 COMPLEX WITH BIOTINYL-5'-AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIOTIN LIGASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 553596; SOURCE 4 STRAIN: A9781; SOURCE 5 GENE: SAOG_00031; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BIOTIN, METABOLISM, BIOTIN CARBOXYL CARRIER PROTEIN, LIGASE-LIGASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.Y.YAP REVDAT 4 20-MAR-24 3V8L 1 REMARK SEQADV REVDAT 3 17-JUL-13 3V8L 1 JRNL REVDAT 2 27-MAR-13 3V8L 1 REMARK REVDAT 1 26-DEC-12 3V8L 0 JRNL AUTH T.P.SOARES DA COSTA,W.TIEU,M.Y.YAP,N.R.PENDINI,S.W.POLYAK, JRNL AUTH 2 D.SEJER PEDERSEN,R.MORONA,J.D.TURNIDGE,J.C.WALLACE, JRNL AUTH 3 M.C.WILCE,G.W.BOOKER,A.D.ABELL JRNL TITL SELECTIVE INHIBITION OF BIOTIN PROTEIN LIGASE FROM JRNL TITL 2 STAPHYLOCOCCUS AUREUS. JRNL REF J.BIOL.CHEM. V. 287 17823 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22437830 JRNL DOI 10.1074/JBC.M112.356576 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25288 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1359 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1823 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2611 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.25000 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): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.133 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.267 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2706 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3655 ; 1.826 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 321 ; 6.987 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;38.804 ;24.929 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 487 ;16.222 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;24.573 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 397 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2045 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1067 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1811 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 211 ; 0.172 ; 0.200 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): 35 ; 0.160 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.183 ; 0.200 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): 1649 ; 1.758 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2574 ; 2.732 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1215 ; 2.144 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1081 ; 3.259 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 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 64 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0924 24.6625 46.3379 REMARK 3 T TENSOR REMARK 3 T11: -0.2651 T22: -0.1156 REMARK 3 T33: -0.1748 T12: 0.1230 REMARK 3 T13: 0.0427 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 5.9235 L22: 6.2756 REMARK 3 L33: 5.0790 L12: -2.4146 REMARK 3 L13: -2.1898 L23: 0.3450 REMARK 3 S TENSOR REMARK 3 S11: -0.0622 S12: -0.3341 S13: 0.2946 REMARK 3 S21: -0.0096 S22: 0.1056 S23: -0.3083 REMARK 3 S31: -0.0016 S32: -0.0834 S33: -0.0434 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 : A 65 A 263 REMARK 3 ORIGIN FOR THE GROUP (A): 40.7912 17.4558 21.7204 REMARK 3 T TENSOR REMARK 3 T11: -0.2348 T22: -0.1268 REMARK 3 T33: -0.1325 T12: 0.0282 REMARK 3 T13: 0.0529 T23: 0.0708 REMARK 3 L TENSOR REMARK 3 L11: 1.8470 L22: 2.9553 REMARK 3 L33: 2.4207 L12: -0.1631 REMARK 3 L13: -0.3664 L23: -0.1007 REMARK 3 S TENSOR REMARK 3 S11: 0.0476 S12: 0.0786 S13: 0.2627 REMARK 3 S21: -0.0504 S22: 0.2290 S23: 0.1730 REMARK 3 S31: -0.3418 S32: -0.2521 S33: -0.2766 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 264 A 321 REMARK 3 ORIGIN FOR THE GROUP (A): 50.4289 18.0004 0.6372 REMARK 3 T TENSOR REMARK 3 T11: -0.0252 T22: -0.2048 REMARK 3 T33: -0.3412 T12: -0.0940 REMARK 3 T13: 0.0663 T23: 0.0797 REMARK 3 L TENSOR REMARK 3 L11: 7.2431 L22: 3.8381 REMARK 3 L33: 7.3953 L12: 0.5497 REMARK 3 L13: -3.0840 L23: -0.7465 REMARK 3 S TENSOR REMARK 3 S11: -0.0801 S12: 0.4870 S13: -0.1768 REMARK 3 S21: -0.3493 S22: 0.2642 S23: -0.1410 REMARK 3 S31: -0.4762 S32: 0.0287 S33: -0.1841 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 3V8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.518 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 39.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 8000, 10% GLYCEROL, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 46.83250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.83250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.97350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.83250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 46.83250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 65.97350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.83250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.83250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.97350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 46.83250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.83250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.97350 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 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: 4260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 93.66500 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 856 LIES ON A SPECIAL POSITION. 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 HIS 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 MET A 0 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 ILE A 271 CG1 CG2 CD1 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 ASN A 278 CG ASN A 278 OD1 0.191 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 254 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 306 NE - CZ - NH1 ANGL. DEV. = -3.7 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 LYS A 2 -37.97 -39.61 REMARK 500 HIS A 54 -5.91 76.30 REMARK 500 LYS A 117 47.81 -146.81 REMARK 500 ASN A 178 13.12 -144.04 REMARK 500 ASP A 183 -121.73 51.98 REMARK 500 ASP A 220 129.26 63.03 REMARK 500 GLU A 221 -128.64 83.56 REMARK 500 ASN A 286 -114.08 52.84 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 BT5 A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CGH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BIOTIN LIGASE FROM MYCOBACTERIUM TUBERCULOSIS REMARK 900 RELATED ID: 1HXD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN REMARK 900 RELATED ID: 2EAY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BIOTIN PROTEIN LIGASE FROM AQUIFEX AEOLICUS REMARK 900 RELATED ID: 3V7C RELATED DB: PDB REMARK 900 RELATED ID: 3V7R RELATED DB: PDB REMARK 900 RELATED ID: 3V7S RELATED DB: PDB REMARK 900 RELATED ID: 3V8J RELATED DB: PDB REMARK 900 RELATED ID: 3V8K RELATED DB: PDB DBREF 3V8L A 0 322 UNP C8N5A9 C8N5A9_STAAU 1 323 SEQADV 3V8L HIS A -6 UNP C8N5A9 EXPRESSION TAG SEQADV 3V8L HIS A -5 UNP C8N5A9 EXPRESSION TAG SEQADV 3V8L HIS A -4 UNP C8N5A9 EXPRESSION TAG SEQADV 3V8L HIS A -3 UNP C8N5A9 EXPRESSION TAG SEQADV 3V8L HIS A -2 UNP C8N5A9 EXPRESSION TAG SEQADV 3V8L HIS A -1 UNP C8N5A9 EXPRESSION TAG SEQRES 1 A 329 HIS HIS HIS HIS HIS HIS MET SER LYS TYR SER GLN ASP SEQRES 2 A 329 VAL LEU GLN LEU LEU TYR LYS ASN LYS PRO ASN TYR ILE SEQRES 3 A 329 SER GLY GLN SER ILE ALA GLU SER LEU ASN ILE SER ARG SEQRES 4 A 329 THR ALA VAL LYS LYS VAL ILE ASP GLN LEU LYS LEU GLU SEQRES 5 A 329 GLY CYS LYS ILE ASP SER VAL ASN HIS LYS GLY HIS LEU SEQRES 6 A 329 LEU GLN GLN LEU PRO ASP ILE TRP TYR GLN GLY ILE ILE SEQRES 7 A 329 ASP GLN TYR THR LYS SER SER ALA LEU PHE ASP PHE SER SEQRES 8 A 329 GLU VAL TYR ASP SER ILE ASP SER THR GLN LEU ALA ALA SEQRES 9 A 329 LYS LYS SER LEU VAL GLY ASN GLN SER SER PHE PHE ILE SEQRES 10 A 329 LEU SER ASP GLU GLN THR LYS GLY ARG GLY ARG PHE ASN SEQRES 11 A 329 ARG HIS TRP SER SER SER LYS GLY GLN GLY LEU TRP MET SEQRES 12 A 329 SER VAL VAL LEU ARG PRO ASN VAL ALA PHE SER MET ILE SEQRES 13 A 329 SER LYS PHE ASN LEU PHE ILE ALA LEU GLY ILE ARG ASP SEQRES 14 A 329 ALA ILE GLN HIS PHE SER GLN ASP GLU VAL LYS VAL LYS SEQRES 15 A 329 TRP PRO ASN ASP ILE TYR ILE ASP ASN GLY LYS VAL CYS SEQRES 16 A 329 GLY PHE LEU THR GLU MET VAL ALA ASN ASN ASP GLY ILE SEQRES 17 A 329 GLU ALA ILE ILE CYS GLY ILE GLY ILE ASN LEU THR GLN SEQRES 18 A 329 GLN LEU GLU ASN PHE ASP GLU SER ILE ARG HIS ARG ALA SEQRES 19 A 329 THR SER ILE GLN LEU HIS ASP LYS ASN LYS LEU ASP ARG SEQRES 20 A 329 TYR GLN PHE LEU GLU ARG LEU LEU GLN GLU ILE GLU LYS SEQRES 21 A 329 ARG TYR ASN GLN PHE LEU THR LEU PRO PHE SER GLU ILE SEQRES 22 A 329 ARG GLU GLU TYR ILE ALA ALA SER ASN ILE TRP ASN ARG SEQRES 23 A 329 THR LEU LEU PHE THR GLU ASN ASP LYS GLN PHE LYS GLY SEQRES 24 A 329 GLN ALA ILE ASP LEU ASP TYR ASP GLY TYR LEU ILE VAL SEQRES 25 A 329 ARG ASP GLU ALA GLY GLU SER HIS ARG LEU ILE SER ALA SEQRES 26 A 329 ASP ILE ASP PHE HET BT5 A 500 38 HETNAM BT5 BIOTINYL-5-AMP FORMUL 2 BT5 C20 H28 N7 O9 P S FORMUL 3 HOH *305(H2 O) HELIX 1 1 TYR A 3 LYS A 15 1 13 HELIX 2 2 SER A 20 ASN A 29 1 10 HELIX 3 3 SER A 31 GLU A 45 1 15 HELIX 4 4 TYR A 67 SER A 77 1 11 HELIX 5 5 SER A 92 LEU A 101 1 10 HELIX 6 6 GLY A 120 ARG A 124 5 5 HELIX 7 7 ALA A 145 SER A 147 5 3 HELIX 8 8 MET A 148 HIS A 166 1 19 HELIX 9 9 GLN A 215 PHE A 219 5 5 HELIX 10 10 ILE A 223 ALA A 227 5 5 HELIX 11 11 SER A 229 ASP A 234 5 6 HELIX 12 12 ASP A 239 LEU A 261 1 23 HELIX 13 13 PHE A 263 ALA A 273 1 11 SHEET 1 A 2 LYS A 48 VAL A 52 0 SHEET 2 A 2 GLY A 56 GLN A 61 -1 O GLN A 60 N LYS A 48 SHEET 1 B 7 PHE A 83 ILE A 90 0 SHEET 2 B 7 PHE A 108 GLN A 115 1 O LEU A 111 N GLU A 85 SHEET 3 B 7 GLY A 133 LEU A 140 -1 O VAL A 139 N PHE A 108 SHEET 4 B 7 GLY A 200 ASN A 211 -1 O ILE A 208 N MET A 136 SHEET 5 B 7 GLY A 185 ASN A 197 -1 N VAL A 195 O GLU A 202 SHEET 6 B 7 ASP A 179 ILE A 182 -1 N ILE A 182 O GLY A 185 SHEET 7 B 7 VAL A 172 LYS A 175 -1 N LYS A 175 O ASP A 179 SHEET 1 C 5 SER A 312 LEU A 315 0 SHEET 2 C 5 LEU A 303 ASP A 307 -1 N LEU A 303 O LEU A 315 SHEET 3 C 5 LYS A 288 LEU A 297 -1 N ILE A 295 O ILE A 304 SHEET 4 C 5 LEU A 281 GLU A 285 -1 N PHE A 283 O PHE A 290 SHEET 5 C 5 ASP A 319 ASP A 321 -1 O ASP A 321 N LEU A 282 CISPEP 1 LYS A 15 PRO A 16 0 -2.55 CISPEP 2 TRP A 176 PRO A 177 0 -6.32 SITE 1 AC1 21 SER A 92 THR A 93 GLN A 115 GLY A 118 SITE 2 AC1 21 ARG A 119 GLY A 120 ARG A 121 ARG A 124 SITE 3 AC1 21 HIS A 125 TRP A 126 SER A 127 MET A 136 SITE 4 AC1 21 ASP A 179 LYS A 186 GLY A 189 ILE A 208 SITE 5 AC1 21 GLY A 209 ASN A 211 ILE A 223 HOH A 880 SITE 6 AC1 21 HOH A 885 CRYST1 93.665 93.665 131.947 90.00 90.00 90.00 P 42 21 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 0.010676 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007579 0.00000