+Open data
-Basic information
Entry | Database: PDB / ID: 3wo9 | ||||||
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Title | Crystal structure of the lamprey variable lymphocyte receptor C | ||||||
Components | Variable lymphocyte receptor C | ||||||
Keywords | IMMUNE SYSTEM / Leucine rich repeat / immunological receptor / Membrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lethenteron camtschaticum (Arctic lamprey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kanda, R. / Sutoh, Y. / Kasamatsu, J. / Maenaka, K. / Kasahara, M. / Ose, T. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Crystal structure of the lamprey variable lymphocyte receptor C reveals an unusual feature in its N-terminal capping module. Authors: Kanda, R. / Sutoh, Y. / Kasamatsu, J. / Maenaka, K. / Kasahara, M. / Ose, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wo9.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wo9.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wo9_validation.pdf.gz | 418.8 KB | Display | wwPDB validaton report |
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Full document | 3wo9_full_validation.pdf.gz | 419.9 KB | Display | |
Data in XML | 3wo9_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3wo9_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/3wo9 ftp://data.pdbj.org/pub/pdb/validation_reports/wo/3wo9 | HTTPS FTP |
-Related structure data
Related structure data | 2o6qS S: Starting model for refinement |
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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: 27544.906 Da / Num. of mol.: 1 / Fragment: VLRC ectodomain, UNP RESIDUES 25-246 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lethenteron camtschaticum (Arctic lamprey) Gene: VLRC / Plasmid: pET-26(b) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: E0D2V6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 3350, 0.2M potassium phosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 29, 2011 / Details: mirrors |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 9798 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 16.63 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 4.1 / Num. unique all: 885 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O6Q Resolution: 2.3→37.469 Å / SU ML: 0.25 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 22.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.6 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→37.469 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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