+Open data
-Basic information
Entry | Database: PDB / ID: 1tcr | |||||||||
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Title | MURINE T-CELL ANTIGEN RECEPTOR 2C CLONE | |||||||||
Components | (ALPHA, BETA T-CELL RECEPTOR (VB8.2DB2JB2.4CB2\; ...) x 2 | |||||||||
Keywords | RECEPTOR / T-CELL / TRANSMEMBRANE / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / molecular replacement/MIR / Resolution: 2.5 Å | |||||||||
Authors | Garcia, K.C. / Degano, M. / Stanfield, R.L. / Wilson, I.A. | |||||||||
Citation | Journal: Science / Year: 1996 Title: An alphabeta T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex. Authors: Garcia, K.C. / Degano, M. / Stanfield, R.L. / Brunmark, A. / Jackson, M.R. / Peterson, P.A. / Teyton, L. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tcr.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tcr.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tcr_validation.pdf.gz | 600.6 KB | Display | wwPDB validaton report |
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Full document | 1tcr_full_validation.pdf.gz | 614.5 KB | Display | |
Data in XML | 1tcr_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1tcr_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/1tcr ftp://data.pdbj.org/pub/pdb/validation_reports/tc/1tcr | HTTPS FTP |
-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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-Components
-ALPHA, BETA T-CELL RECEPTOR (VB8.2DB2JB2.4CB2\; ... , 2 types, 2 molecules AB
#1: Protein | Mass: 22298.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: T-LYMPHOCYTES / Production host: Drosophila melanogaster (fruit fly) / References: EMBL: X01134, UniProt: P01738*PLUS |
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#2: Protein | Mass: 26284.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: T-LYMPHOCYTES / Production host: Drosophila melanogaster (fruit fly) / References: GenBank: 1791255 |
-Sugars , 4 types, 4 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 25 molecules
#7: Chemical | #8: 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: 2.95 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 6.4 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 18337 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.9 / % possible all: 99.3 |
Reflection shell | *PLUS % possible obs: 99.3 % |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement/MIR Starting model: ISOLATED BETA CHAIN, V(ALPHA) DOMAIN Highest resolution: 2.5 Å / Cross valid method: RFREE / σ(F): 2 Details: REMARK: MANY RESIDUES OF CHAIN A HAVE HIGHER TEMPERATURE FACTORS ASSOCIATED WITH THEM THAN THE REST OF THE MOLECULE. THE IMPLICATIONS ARE DISCUSSED IN THE ARTICLE. RESIDUES A 185 - A 213 AND ...Details: REMARK: MANY RESIDUES OF CHAIN A HAVE HIGHER TEMPERATURE FACTORS ASSOCIATED WITH THEM THAN THE REST OF THE MOLECULE. THE IMPLICATIONS ARE DISCUSSED IN THE ARTICLE. RESIDUES A 185 - A 213 AND THE CARBOHYDRATE RESIDUE 200 HAVE ASSOCIATED HIGH TEMPERATURE FACTORS. THESE RESIDUES ARE NOT IN CONTACT WITH OTHER SECONDARY STRUCTURE ELEMENTS OR SYMMETRY RELATED MOLECULES. NEVERTHELESS, THE ELECTRON DENSITY ASSOCIATED WITH THE ATOMS IS UNAMBIGUOUS AND OF GOOD QUALITY.
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Displacement parameters | Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.224 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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