+Open data
-Basic information
Entry | Database: PDB / ID: 1sbb | ||||||
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Title | T-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SUPERANTIGEN SEB | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T CELL RECEPTOR / SUPERANTIGEN / COMPLEX | ||||||
Function / homology | Function and homology information alpha-beta T cell receptor complex / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / toxin activity / antibacterial humoral response / blood microparticle / extracellular exosome / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Li, H. / Mariuzza, R.A. | ||||||
Citation | Journal: Immunity / Year: 1998 Title: Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B. Authors: Li, H. / Llera, A. / Tsuchiya, D. / Leder, L. / Ysern, X. / Schlievert, P.M. / Karjalainen, K. / 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 | 1sbb.cif.gz | 204.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sbb.ent.gz | 161.8 KB | Display | PDB format |
PDBx/mmJSON format | 1sbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sbb_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 1sbb_full_validation.pdf.gz | 479 KB | Display | |
Data in XML | 1sbb_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 1sbb_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/1sbb ftp://data.pdbj.org/pub/pdb/validation_reports/sb/1sbb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-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, UniProt: P01852*PLUS #2: Protein | Mass: 28411.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN9220 / Production host: Escherichia coli (E. coli) / References: UniProt: P01552 #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: 2.5 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: CRYSTALLIZATION CONDITIONS: 10% PEG 8000 0.1M TRIS-HCL, PH8.5 | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 6 % | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: used to seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Aug 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 34934 / % possible obs: 91.5 % / Redundancy: 9 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / Rsym value: 0.36 / % possible all: 79.1 |
Reflection | *PLUS Num. measured all: 325939 |
Reflection shell | *PLUS % possible obs: 79.1 % / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SE4 AND 1BEC Resolution: 2.4→6 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.45 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 15
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / σ(F): 2 / % reflection Rfree: 8.2 % / Rfactor obs: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å / Rfactor Rfree: 0.442 / % reflection Rfree: 6.7 % / Rfactor Rwork: 0.356 |