HEADER TRANSFERASE 15-JUL-03 1OJQ TITLE THE CRYSTAL STRUCTURE OF C3STAU2 FROM S. AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 OTHER_DETAILS: SYNTHETIC GENE KEYWDS ADP-RIBOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.R.EVANS,J.M.SUTTON,D.E.HOLLOWAY,J.AYRISS,C.C.SHONE,K.R.ACHARYA REVDAT 5 08-MAY-24 1OJQ 1 REMARK REVDAT 4 22-MAY-19 1OJQ 1 REMARK REVDAT 3 24-FEB-09 1OJQ 1 VERSN REVDAT 2 13-NOV-03 1OJQ 1 JRNL REVDAT 1 28-AUG-03 1OJQ 0 JRNL AUTH H.R.EVANS,J.M.SUTTON,D.E.HOLLOWAY,J.AYRISS,C.C.SHONE, JRNL AUTH 2 K.R.ACHARYA JRNL TITL THE CRYSTAL STRUCTURE OF C3STAU2 FROM STAPHYLOCOCCUS AUREUS JRNL TITL 2 AND ITS COMPLEX WITH NAD JRNL REF J.BIOL.CHEM. V. 278 45924 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12933793 JRNL DOI 10.1074/JBC.M307719200 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.170 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 872 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 22327 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.156 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 19621 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 284 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1934.9 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7863 REMARK 3 NUMBER OF RESTRAINTS : 6859 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.037 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.047 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.062 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS (BRUNGER ET AL) WAS USED IN THE REMARK 3 INITIAL STAGES OF REFINEMENT. RESIDUES 197-199 ARE SLIGHTLY REMARK 3 DISORDERED AND MODELLED ON THE BASIS OF WEAK DENSITY. THE REMARK 3 EXTREMITIES OF SIDE CHAINS 85, 94,170 AND 200 HAVE BEEN MODELLED REMARK 3 AT ZERO OCCUPENCY DUE TO INSUFFICIENT DENSITY. REMARK 4 REMARK 4 1OJQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1290013076. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22478 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 0.1M SODIUM CACODYLATE REMARK 280 BUFFER PH 6.5, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 19.80800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.49200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.26250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.49200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.80800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.26250 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 24 CE NZ REMARK 470 ARG A 85 CD NE CZ NH1 NH2 REMARK 470 SER A 94 OG REMARK 470 GLU A 116 CG CD OE1 OE2 REMARK 470 LYS A 200 CE NZ 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 ASN A 199 C - N - CA ANGL. DEV. = 29.5 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 ASN A 39 82.46 -166.64 REMARK 500 SER A 197 -147.55 -57.13 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 A2027 DISTANCE = 6.29 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GXY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE REMARK 900 ART2.2 REMARK 900 RELATED ID: 1GXZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE REMARK 900 ART2.2 REMARK 900 RELATED ID: 1GZE RELATED DB: PDB REMARK 900 STRUCTURE OF THE CLOSTRIDIUM BOTULINUM C3 EXOENZYME (L177C MUTANT) REMARK 900 RELATED ID: 1GZF RELATED DB: PDB REMARK 900 STRUCTURE OF THE CLOSTRIDIUM BOTULINUM C3 EXOENZYME (WILD-TYPE) IN REMARK 900 COMPLEX WITH NAD REMARK 900 RELATED ID: 1GY0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE REMARK 900 ART2.2 REMARK 900 RELATED ID: 1OG1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE REMARK 900 ART2.2 IN COMPLEX WITH TAD REMARK 900 RELATED ID: 1OG3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE REMARK 900 ART2.2 MUTANT E189I IN KOMPLEX WITH NAD REMARK 900 RELATED ID: 1OG4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP -RIBOSYLTRANSFERASE REMARK 900 ART2.2 MUTANT E189A IN COMPLEX WITH NADH REMARK 900 RELATED ID: 1OJZ RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF C3STAU2 FROM S. AUREUS IN COMPLEX WITH NAD DBREF 1OJQ A 1 212 UNP Q9ADS9 Q9ADS9 1 212 SEQRES 1 A 212 ALA GLU THR LYS ASN PHE THR ASP LEU VAL GLU ALA THR SEQRES 2 A 212 LYS TRP GLY ASN SER LEU ILE LYS SER ALA LYS TYR SER SEQRES 3 A 212 SER LYS ASP LYS MET ALA ILE TYR ASN TYR THR LYS ASN SEQRES 4 A 212 SER SER PRO ILE ASN THR PRO LEU ARG SER ALA ASN GLY SEQRES 5 A 212 ASP VAL ASN LYS LEU SER GLU ASN ILE GLN GLU GLN VAL SEQRES 6 A 212 ARG GLN LEU ASP SER THR ILE SER LYS SER VAL THR PRO SEQRES 7 A 212 ASP SER VAL TYR VAL TYR ARG LEU LEU ASN LEU ASP TYR SEQRES 8 A 212 LEU SER SER ILE THR GLY PHE THR ARG GLU ASP LEU HIS SEQRES 9 A 212 MET LEU GLN GLN THR ASN ASN GLY GLN TYR ASN GLU ALA SEQRES 10 A 212 LEU VAL SER LYS LEU ASN ASN LEU MET ASN SER ARG ILE SEQRES 11 A 212 TYR ARG GLU ASN GLY TYR SER SER THR GLN LEU VAL SER SEQRES 12 A 212 GLY ALA ALA LEU ALA GLY ARG PRO ILE GLU LEU LYS LEU SEQRES 13 A 212 GLU LEU PRO LYS GLY THR LYS ALA ALA TYR ILE ASP SER SEQRES 14 A 212 LYS GLU LEU THR ALA TYR PRO GLY GLN GLN GLU VAL LEU SEQRES 15 A 212 LEU PRO ARG GLY THR GLU TYR ALA VAL GLY SER VAL LYS SEQRES 16 A 212 LEU SER ASP ASN LYS ARG LYS ILE ILE ILE THR ALA VAL SEQRES 17 A 212 VAL PHE LYS LYS FORMUL 2 HOH *284(H2 O) HELIX 1 1 ASP A 8 LYS A 24 1 17 HELIX 2 2 SER A 26 ASN A 39 1 14 HELIX 3 3 SER A 40 ALA A 50 1 11 HELIX 4 4 ASP A 53 LEU A 57 5 5 HELIX 5 5 SER A 58 LYS A 74 1 17 HELIX 6 6 ASN A 88 ILE A 95 5 8 HELIX 7 7 THR A 99 GLN A 107 1 9 HELIX 8 8 ASN A 115 ASN A 127 1 13 SHEET 1 AA 5 VAL A 81 LEU A 87 0 SHEET 2 AA 5 ILE A 152 LEU A 158 -1 O ILE A 152 N LEU A 87 SHEET 3 AA 5 ILE A 203 VAL A 209 1 O ILE A 203 N GLU A 153 SHEET 4 AA 5 THR A 187 LEU A 196 -1 O ALA A 190 N VAL A 208 SHEET 5 AA 5 ILE A 130 GLU A 133 -1 O TYR A 131 N TYR A 189 SHEET 1 AB 3 SER A 137 GLN A 140 0 SHEET 2 AB 3 GLU A 180 LEU A 183 -1 O VAL A 181 N THR A 139 SHEET 3 AB 3 ALA A 165 TYR A 166 -1 O ALA A 165 N LEU A 182 CRYST1 39.616 64.525 74.984 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025242 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013336 0.00000