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Yorodumi- PDB-3mc0: Crystal Structure of Staphylococcal Enterotoxin G (SEG) in Comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mc0 | ||||||
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Title | Crystal Structure of Staphylococcal Enterotoxin G (SEG) in Complex with a Mouse T-cell Receptor beta Chain | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Exotoxin | ||||||
Function / homology | Function and homology information T cell receptor complex / toxin activity / adaptive immune response / extracellular region Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Fernandez, M.M. / Cho, S. / Robinson, H. / Mariuzza, R.A. / Malchiodi, E.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal structure of staphylococcal enterotoxin G (SEG) in complex with a mouse T-cell receptor {beta} chain. Authors: Fernandez, M.M. / Cho, S. / De Marzi, M.C. / Kerzic, M.C. / Robinson, H. / Mariuzza, R.A. / Malchiodi, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mc0.cif.gz | 155.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mc0.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/3mc0 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/3mc0 | HTTPS FTP |
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-Related structure data
Related structure data | 3oweC 1jckS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11765.953 Da / Num. of mol.: 2 / Fragment: unp residues 31-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A2NTY6 #2: Protein | Mass: 27846.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Fc30 isolate / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D0EMB6 #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium acetate 1.4 M protein concentration 7.5 mg/ml, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2006 Details: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror. |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→29.9 Å / Num. obs: 68880 / Rmerge(I) obs: 0.084 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1jck Resolution: 2→29.9 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.937 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.153 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
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