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Yorodumi- PDB-1i4p: CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN C2 AT 100K CRYSTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i4p | ||||||
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Title | CRYSTAL STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN C2 AT 100K CRYSTALLIZED AT PH 5.5 | ||||||
Components | ENTEROTOXIN TYPE C-2 | ||||||
Keywords | TOXIN / ENTEROTOXIN / SUPERANTIGEN / ZINC BINDING / IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kumaran, D. / Swaminathan, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of staphylococcal enterotoxin C2 at various pH levels. Authors: Kumaran, D. / Eswaramoorthy, S. / Furey, W. / Sax, M. / Swaminathan, S. #1: Journal: Nat.Struct.Biol. / Year: 1995 Title: Residues Defining V-Beta Specificity in Staphylococcal Enterotoxins Authors: Swaminathan, S. / Furey, W. / Pletcher, J. / Sax, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Preliminary X-Ray Studies on Two New Crystal Forms of Staphylococcal Enterotoxin C2 Authors: Swaminathan, S. / Furey, W. / Pletcher, J. / Sax, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i4p.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i4p.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i4p_validation.pdf.gz | 422.1 KB | Display | wwPDB validaton report |
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Full document | 1i4p_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 1i4p_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 1i4p_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/1i4p ftp://data.pdbj.org/pub/pdb/validation_reports/i4/1i4p | HTTPS FTP |
-Related structure data
Related structure data | 1cqvC 1i4qC 1i4rC 1i4xC 1se2S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 27622.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P34071 |
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#2: Chemical | ChemComp-ZN / |
#3: 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: 2.15 Å3/Da / Density % sol: 43.3 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 8000, magnesium Acetate, cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 3 R.T. | |||||||||||||||||||||||||
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: NSLS / Beamline: X12B / Wavelength: 0.978 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Jul 17, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 15905 / % possible obs: 78.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.99→2.02 Å / % possible all: 30.5 |
Reflection | *PLUS Num. measured all: 67434 |
Reflection shell | *PLUS % possible obs: 30.5 % / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SE2 Resolution: 2→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |