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Yorodumi- PDB-2aq1: Crystal structure of T-cell receptor V beta domain variant comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aq1 | ||||||
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Title | Crystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3 mutant | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T-CELL RECEPTOR / STAPHYLOCOCCAL ENTEROTOXIN C3 / SUPERANTIGEN / COMPLEX (TOXIN-RECEPTOR) | ||||||
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 | Mus musculus (house mouse) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cho, S. / Swaminathan, C.P. / Yang, J. / Kerzic, M.C. / Guan, R. / Kieke, M.C. / Kranz, D.M. / Mariuzza, R.A. / Sundberg, E.J. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction. Authors: Cho, S. / Swaminathan, C.P. / Yang, J. / Kerzic, M.C. / Guan, R. / Kieke, M.C. / Kranz, D.M. / Mariuzza, R.A. / Sundberg, E.J. | ||||||
History |
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Remark 600 | HETEROGEN PORTIONS OF THE DENSITY WAS COMPRISED OF PEG BUT THE COMPLETE MOLECULE COULD NOT BE TRACED. | ||||||
Remark 999 | SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE CHAINS A, C, E and G AT THE ...SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE FOR THE CHAINS A, C, E and G AT THE TIME OF PROCESSING THIS ENTRY. THE FIVE SEC3 WILD TYPE RESIDUES AT POSITIONS 102-106 (GKVTG) IN CHAINS B, D, F AND H ARE REPLACED BY THREE RESIDUES (WWH). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aq1.cif.gz | 288.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aq1.ent.gz | 242.1 KB | Display | PDB format |
PDBx/mmJSON format | 2aq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aq1_validation.pdf.gz | 480.5 KB | Display | wwPDB validaton report |
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Full document | 2aq1_full_validation.pdf.gz | 510.2 KB | Display | |
Data in XML | 2aq1_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 2aq1_validation.cif.gz | 80.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/2aq1 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/2aq1 | HTTPS FTP |
-Related structure data
Related structure data | 2apbC 2apfC 2aptC 2apvC 2apwC 2apxC 2aq2C 2aq3C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 12174.466 Da / Num. of mol.: 4 / Mutation: G17E,A52V,S54N,K66E,E80V,L81S,T87S,G96V 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)pLysS / References: UniProt: P04213 #2: Protein | Mass: 27690.033 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0L5 #3: 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: 2.8 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.2M tri-ammonium citrate, 0.3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0722 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.5 % / Number: 81743 / Rmerge(I) obs: 0.034 / Χ2: 1.48 / D res high: 2.1 Å / D res low: 40 Å / % possible obs: 89.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.1→40 Å / Num. obs: 81743 / % possible obs: 89.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2.5 % / Rmerge(I) obs: 0.034 / Χ2: 1.48 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / % possible obs: 66 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.222 / Num. measured obs: 5983 / Χ2: 1.054 / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.553 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.303 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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