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- PDB-5fka: Crystal structure of staphylococcal enterotoxin E in complex with... -
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Open data
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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 | ||||||
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![]() | IMMUNE SYSTEM / SUPERANTIGEN / STAPHYLCOCOCCAL ENTEROTOXIN / T CELL RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX | ||||||
Function / homology | ![]() T cell receptor complex / immune system process / toxin activity / adaptive immune response / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rodstrom, K.E.J. / Regenthal, P. / Lindkvist-Petersson, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.6 KB | Display | ![]() |
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PDB format | ![]() | 109.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5fk9C ![]() 4udtS ![]() 4uduS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
#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.) ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has protein modification | Y |
Sequence details | THE STRUCTURE CONTAINS EXTRACELLULAR TCR ALPHA VARIABLE AND CONSTANT DOMAINS. DATABASE REFERENCE IS ...THE STRUCTURE CONTAINS EXTRACELLU |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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