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Yorodumi- PDB-1uns: IDENTIFICATION OF A SECONDARY ZINC-BINDING SITE IN STAPHYLOCOCCAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uns | ||||||
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Title | IDENTIFICATION OF A SECONDARY ZINC-BINDING SITE IN STAPHYLOCOCCAL ENTEROTOXIN C2: IMPLICATIONS FOR SUPERANTIGEN RECOGNITION | ||||||
Components | ENTEROTOXIN TYPE C-2 | ||||||
Keywords | TOXIN / SUPERANTIGEN / ENTEROTOXIN / ZINC-BINDING SITE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Papageorgiou, A.C. / Baker, M.D. / McLeod, J.D. / Goda, S. / Sansom, D.M. / Tranter, H.S. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Identification of a Secondary Zinc-Binding Site in Staphylococcal Enterotoxin C2: Implications for Superantigen Recognition Authors: Papageorgiou, A.C. / Baker, M.D. / Mcleod, J.D. / Goda, S. / Manzotti, C.N. / Sanson, D.M. / Tranter, H.S. / Acharya, K.R. #1: Journal: Structure / Year: 1995 Title: Structure of the Superantigen Enterotoxin C2 from Staphylococcus Aureus Reveals a Zinc-Binding Site Authors: Papageorgiou, A.C. / Acharya, K.R. / Shapiro, R. / Passalacqua, E.F. / Brehm, R.D. / Tranter, H.S. #2: Journal: Bacterial Superantigens: Structure, Function and Therapeutic Potential Year: 1995 Title: Molecular Topology is Important for the Function of Staphylococcal Superantigens Authors: Tranter, H. / Brehm, R.D. / Acharya, K.R. #3: Journal: Nature / Year: 1994 Title: Structural Basis of Superantigen Action Inferred from Crystal Structure of Toxic-Shock Syndrome Toxin-1 Authors: Acharya, K.R. / Passalacqua, E.F. / Jones, E.Y. / Harlos, K. / Stuart, D.I. / Brehm, R.D. / Tranter, H.S. #4: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and Preliminary X-Ray Analysis of a Microbial Superantigen Staphylococcal Enterotoxin C2 Authors: Passalacqua, E.F. / Brehm, R.D. / Acharya, K.R. / Tranter, H.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uns.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uns.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 1uns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uns_validation.pdf.gz | 363.9 KB | Display | wwPDB validaton report |
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Full document | 1uns_full_validation.pdf.gz | 367.6 KB | Display | |
Data in XML | 1uns_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1uns_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/un/1uns ftp://data.pdbj.org/pub/pdb/validation_reports/un/1uns | HTTPS FTP |
-Related structure data
Related structure data | 1steS S: Starting model for refinement |
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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 | #3: Water | ChemComp-HOH / | Compound details | ZINC ION A1237 IS TETRAHEDRALLY COORDINATED TO HIS 118, HIS 122 ASP 83 AND ASP 9 FROM A SYMMETRY ...ZINC ION A1237 IS TETRAHEDRA | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.46 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.88 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 16364 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.078 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. measured all: 80816 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.06 Å / % possible obs: 72.1 % / Rmerge(I) obs: 0.297 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1STE Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 19.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å / Num. reflection obs: 16330 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.006 |