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Yorodumi- PDB-2aq3: Crystal structure of T-cell receptor V beta domain variant comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aq3 | ||||||
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Title | Crystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T-CELL RECEPTOR V BETA DOMAIN / STAPHLOCOCCAL ENTEROTOXIN C3 / COMPLEX STRUCTURE | ||||||
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: 2.3 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. TWO SEC3 WILD TYPE RESIDUES AT POSITIONS 100 AND 101 IN THE SEQUENCE DATABASE REFERENCE (NV) WERE REMOVED IN CHAINS B, D, F AND H. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aq3.cif.gz | 281.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aq3.ent.gz | 235.8 KB | Display | PDB format |
PDBx/mmJSON format | 2aq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aq3_validation.pdf.gz | 500.2 KB | Display | wwPDB validaton report |
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Full document | 2aq3_full_validation.pdf.gz | 635.8 KB | Display | |
Data in XML | 2aq3_validation.xml.gz | 67.2 KB | Display | |
Data in CIF | 2aq3_validation.cif.gz | 90.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/2aq3 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/2aq3 | HTTPS FTP |
-Related structure data
Related structure data | 2apbC 2apfC 2aptC 2apvC 2apwC 2apxC 2aq1C 2aq2C C: citing same article (ref.) |
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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: 12121.383 Da / Num. of mol.: 4 / Mutation: G17E, L81S 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: 27409.756 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: 55.7 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.072 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2004 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 63758 / % possible obs: 73.66 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2.4 % / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2.3→2.36 Å / % possible all: 73.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.872 / SU B: 13.176 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the limited electron densities in a few regions, some adjacent residues in the structure appear to be linked by long C-N linkages. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the limited electron densities in a few regions, some adjacent residues in the structure appear to be linked by long C-N linkages. These include G63 and Y65 in chains A, C, E; residues Y101 and F108 in chains A, C, E; residues V101 and V102 in chain H.
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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: 45.433 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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