+Open data
-Basic information
Entry | Database: PDB / ID: 1h5b | ||||||
---|---|---|---|---|---|---|---|
Title | T cell receptor Valpha11 (AV11S5) domain | ||||||
Components | (MURINE T CELL RECEPTOR (TCR) VALPHA ...) x 3 | ||||||
Keywords | T CELL RECEPTOR / IMMUNE RESPONSE / IMMUNOGLOBULIN FOLD | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Machius, M. / Cianga, P. / Deisenhofer, J. / Sally Ward, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structure of a T Cell Receptor Valpha11 (Av11S5) Domain: New Canonical Forms for the First and Second Complementarity Determining Regions Authors: Machius, M. / Cianga, P. / Deisenhofer, J. / Ward, E.S. #1: Journal: J.Mol.Biol. / Year: 2000 Title: Canonical Structures for the Hypervariable Regions of T Cell Ab Receptors Authors: Al-Lazikani, B. / Lesk, A.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1h5b.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1h5b.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 1h5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h5b_validation.pdf.gz | 400.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1h5b_full_validation.pdf.gz | 408.8 KB | Display | |
Data in XML | 1h5b_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1h5b_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/1h5b ftp://data.pdbj.org/pub/pdb/validation_reports/h5/1h5b | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-MURINE T CELL RECEPTOR (TCR) VALPHA ... , 3 types, 4 molecules ABDC
#1: Protein | Mass: 12432.696 Da / Num. of mol.: 1 / Fragment: V-ALPHA DOMAIN VA85.33 (AV11S5-AJ17) Source method: isolated from a genetically manipulated source Details: C-TERMINAL HEXA-HISTIDINE TAG / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: QCII85.33 VALPHAPELBHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BMH71-18 | ||
---|---|---|---|
#2: Protein | Mass: 12474.799 Da / Num. of mol.: 2 / Fragment: V-ALPHA DOMAIN VA85.33 (AV11S5-AJ17) Source method: isolated from a genetically manipulated source Details: C-TERMINAL HEXA-HISTIDINE TAG / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: QCII85.33 VALPHAPELBHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BMH71-18 #3: Protein | | Mass: 12490.799 Da / Num. of mol.: 1 / Fragment: V-ALPHA DOMAIN VA85.33 (AV11S5-AJ17) Source method: isolated from a genetically manipulated source Details: C-TERMINAL HEXA-HISTIDINE TAG / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: QCII85.33 VALPHAPELBHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BMH71-18 |
-Non-polymers , 3 types, 219 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.1 % / Description: SPOTS HAD SMEARY APPEARANCE AT HIGH RESOLUTION | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion / pH: 5.5 Details: 20C, VAPOR DIFFUSION, 3 UL PROTEIN (5 MG/ML IN 50 MM TRIS/CL, 100 MM NACL, PH 8.0) + 3 UL RESERVOIR SOLUTION (100 MM SODIUM CITRATE/HCL, 1.4-1.7 M LITHIUM CHLORIDE, PH 5.0-6.0) EQUILIBRATED ...Details: 20C, VAPOR DIFFUSION, 3 UL PROTEIN (5 MG/ML IN 50 MM TRIS/CL, 100 MM NACL, PH 8.0) + 3 UL RESERVOIR SOLUTION (100 MM SODIUM CITRATE/HCL, 1.4-1.7 M LITHIUM CHLORIDE, PH 5.0-6.0) EQUILIBRATED AGAINST 1 ML OF RESERVOIR SOLUTION. | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 |
Detector | Type: APS1 / Detector: CCD / Date: Feb 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→72.34 Å / Num. obs: 45847 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 3.1 / % possible all: 97.9 |
Reflection shell | *PLUS % possible obs: 97.9 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.85→39.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1253020.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.5957 Å2 / ksol: 0.385249 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→39.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|