+Open data
-Basic information
Entry | Database: PDB / ID: 1jck | ||||||
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Title | T-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SEC3 SUPERANTIGEN | ||||||
Components |
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Keywords | COMPLEX (TOXIN/RECEPTOR) / T-CELL / RECEPTOR / TRANSMEMBRANE / GLYCOPROTEIN / ENTEROTOXIN / TOXIN / SUPERANTIGEN / COMPLEX (TOXIN-RECEPTOR) / COMPLEX (TOXIN-RECEPTOR) complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Fields, B.A. / Mariuzza, R.A. | ||||||
Citation | Journal: Nature / Year: 1996 Title: Crystal structure of a T-cell receptor beta-chain complexed with a superantigen. Authors: Fields, B.A. / Malchiodi, E.L. / Li, H. / Ysern, X. / Stauffacher, C.V. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A. #1: Journal: Science / Year: 1995 Title: Crystal Structure of the Beta Chain of a T Cell Antigen Receptor Authors: Bentley, G.A. / Boulot, G. / Karjalainen, K. / Mariuzza, R.A. #2: Journal: J.Exp.Med. / Year: 1995 Title: Superantigen Binding to a T Cell Receptor Beta Chain of Known Three-Dimensional Structure Authors: Malchiodi, E.L. / Eisenstein, E. / Fields, B.A. / Ohlendorf, D.H. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A. #3: Journal: Science / Year: 1995 Title: Crystal Structure of the V Alpha Domain of a T Cell Antigen Receptor Authors: Fields, B.A. / Ober, B. / Malchiodi, E.L. / Lebedeva, M.I. / Braden, B.C. / Ysern, X. / Kim, J.K. / Shao, X. / Ward, E.S. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jck.cif.gz | 177 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jck.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/1jck ftp://data.pdbj.org/pub/pdb/validation_reports/jc/1jck | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (-1), |
-Components
#1: Protein | Mass: 26568.490 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Mutation: N24Q, N74Q, N121Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: GenBank: 1791255 #2: Protein | Mass: 27664.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: FRI913 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0L5 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: SOLUTION OF 20% PEG1000, 0.1M MGCL2, 0.025% AGAROSE, 0.1M TRIS-HCL PH 6.5 MIXED WITH AN EQUAL VOLUME OF PROTEIN SOLUTION (10MG/ML IN 20MM TRIS-HCL, 25MM NACL, PH 7.5). HANGING DROP METHOD., ...Details: SOLUTION OF 20% PEG1000, 0.1M MGCL2, 0.025% AGAROSE, 0.1M TRIS-HCL PH 6.5 MIXED WITH AN EQUAL VOLUME OF PROTEIN SOLUTION (10MG/ML IN 20MM TRIS-HCL, 25MM NACL, PH 7.5). HANGING DROP METHOD., vapor diffusion - hanging drop PH range: 6.5-7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Highest resolution: 3.5 Å / Num. obs: 11314 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.5→3.56 Å / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.7 / % possible all: 81.3 |
Reflection | *PLUS Num. measured all: 57553 |
Reflection shell | *PLUS % possible obs: 81.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CRYSTAL STRUCTURES OF SEC3 AND TCR BETA Resolution: 3.5→8 Å / Isotropic thermal model: TWO B-FACTORS PER RESIDUE / Cross valid method: FREE R / σ(F): 1 Details: ATOMS ASSIGNED ZERO OCCUPANCY WERE NOT PRESENT IN ELECTRON DENSITY PRESUMABLY BECAUSE OF THE LOW RESOLUTION. HOWEVER, THESE ATOMS WERE LOCATED IN THE CRYSTAL STRUCTURES OF THE UNCOMPLEXED ...Details: ATOMS ASSIGNED ZERO OCCUPANCY WERE NOT PRESENT IN ELECTRON DENSITY PRESUMABLY BECAUSE OF THE LOW RESOLUTION. HOWEVER, THESE ATOMS WERE LOCATED IN THE CRYSTAL STRUCTURES OF THE UNCOMPLEXED COMPONENTS AND ARE THEREFORE INCLUDED IN THE MODEL.
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Displacement parameters | Biso mean: 33.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT TWO-FOLD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.57 Å / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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