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Yorodumi- PDB-5fka: Crystal structure of staphylococcal enterotoxin E in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fka | ||||||
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Title | Crystal structure of staphylococcal enterotoxin E in complex with a T cell receptor | ||||||
Components |
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Keywords | IMMUNE SYSTEM / SUPERANTIGEN / STAPHYLCOCOCCAL ENTEROTOXIN / T CELL RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX | ||||||
Function / homology | Function and homology information T cell receptor complex / toxin activity / adaptive immune response / cell surface receptor signaling pathway / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) STAPHYLOCOCCUS AUREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rodstrom, K.E.J. / Regenthal, P. / Lindkvist-Petersson, K. | ||||||
Citation | Journal: Sci.Rep. / Year: 2016 Title: Two Common Structural Motifs for Tcr Recognition by Staphylococcal Enterotoxins. Authors: Rodstrom, K.E.J. / Regenthal, P. / Bahl, C. / Ford, A. / Baker, D. / Lindkvist-Petersson, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fka.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fka.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fka_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 5fka_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 5fka_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 5fka_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/5fka ftp://data.pdbj.org/pub/pdb/validation_reports/fk/5fka | HTTPS FTP |
-Related structure data
Related structure data | 5fk9C 4udtS 4uduS 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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Unit cell |
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-Components
#1: Protein | Mass: 22812.125 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN DOMAINS Source method: isolated from a genetically manipulated source Details: VARIABLE DOMAIN TRAV22 AND CONSTANT DOMAIN TRAC1 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A0A0B4J277*PLUS |
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#2: Protein | Mass: 27765.832 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN DOMAINS Source method: isolated from a genetically manipulated source Details: VARIABLE DOMAIN TRBV7-9 AND CONSTANT DOMAIN TRBC2 / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A0A5A3*PLUS |
#3: Protein | Mass: 26806.947 Da / Num. of mol.: 1 / Fragment: OB DOMAIN AND BETA GRASP DOMAIN, RESIDUES 1-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Gene: ENTA / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): UL 635 / References: UniProt: P12993 |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Sequence details | THE STRUCTURE CONTAINS EXTRACELLULAR TCR ALPHA VARIABLE AND CONSTANT DOMAINS. DATABASE REFERENCE IS ...THE STRUCTURE CONTAINS EXTRACELLU |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.96 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 25% W/V PEG 3350, 0.1 M GLYCINE PH 9.0, 0.1 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97625 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Details: TOROIDAL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.78 Å / Num. obs: 26772 / % possible obs: 98.8 % / Observed criterion σ(I): 1.9 / Redundancy: 6.6 % / Biso Wilson estimate: 49.35 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4UDU, 4UDT Resolution: 2.4→45.78 Å / Cor.coef. Fo:Fc: 0.9208 / Cor.coef. Fo:Fc free: 0.8848 / SU R Cruickshank DPI: 0.477 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.492 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.256
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Displacement parameters | Biso mean: 38.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.326 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.5 Å / Total num. of bins used: 13
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