+Open data
-Basic information
Entry | Database: PDB / ID: 1ojq | ||||||
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Title | The crystal structure of C3stau2 from S. aureus | ||||||
Components | ADP-RIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / ADP-RIBOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information NAD+-protein ADP-ribosyltransferase activity / nucleotide binding / extracellular region Similarity search - Function | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Evans, H.R. / Sutton, J.M. / Holloway, D.E. / Ayriss, J. / Shone, C.C. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The Crystal Structure of C3Stau2 from Staphylococcus Aureus and its Complex with Nad Authors: Evans, H.R. / Sutton, J.M. / Holloway, D.E. / Ayriss, J. / Shone, C.C. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ojq.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ojq.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ojq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ojq_validation.pdf.gz | 360.6 KB | Display | wwPDB validaton report |
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Full document | 1ojq_full_validation.pdf.gz | 362.4 KB | Display | |
Data in XML | 1ojq_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1ojq_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/1ojq ftp://data.pdbj.org/pub/pdb/validation_reports/oj/1ojq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23666.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9ADS9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 30% PEG 8000, 0.1M SODIUM CACODYLATE BUFFER PH 6.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.6 / PH range high: 6.4 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 22, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 22478 / % possible obs: 98.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.68→1.74 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.3 / % possible all: 97.5 |
Reflection | *PLUS Highest resolution: 1.68 Å / Num. obs: 22619 / % possible obs: 99.4 % / Num. measured all: 409845 / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 97.5 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→50 Å / Num. parameters: 7863 / Num. restraintsaints: 6859 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: CNS (BRUNGER ET AL) WAS USED IN THE INITIAL STAGES OF REFINEMENT. RESIDUES 197-199 ARE SLIGHTLY DISORDERED AND MODELLED ON THE BASIS OF WEAK DENSITY. THE EXTREMITIES OF SIDE CHAINS 85, ...Details: CNS (BRUNGER ET AL) WAS USED IN THE INITIAL STAGES OF REFINEMENT. RESIDUES 197-199 ARE SLIGHTLY DISORDERED AND MODELLED ON THE BASIS OF WEAK DENSITY. THE EXTREMITIES OF SIDE CHAINS 85, 94,170 AND 200 HAVE BEEN MODELLED AT ZERO OCCUPENCY DUE TO INSUFFICIENT DENSITY.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum non hydrogen: 1934.98 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.17 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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