+Open data
-Basic information
Entry | Database: PDB / ID: 4po4 | ||||||
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Title | Crystal Structure of Lampetra planeri VLRC | ||||||
Components | Lampetra planeri VLRC | ||||||
Keywords | IMMUNE SYSTEM / Jawless Vertebrate / VLRC / Leucine Rich Repeat / Variable Lymphocyte Receptor / Antigen Binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lampetra planeri (European brook lamprey) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Gao, M.M. / Mariuzza, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Selection of the lamprey VLRC antigen receptor repertoire. Authors: Holland, S.J. / Gao, M. / Hirano, M. / Iyer, L.M. / Luo, M. / Schorpp, M. / Cooper, M.D. / Aravind, L. / Mariuzza, R.A. / Boehm, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4po4.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4po4.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 4po4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4po4_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 4po4_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 4po4_validation.xml.gz | 21 KB | Display | |
Data in CIF | 4po4_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/4po4 ftp://data.pdbj.org/pub/pdb/validation_reports/po/4po4 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24654.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lampetra planeri (European brook lamprey) Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A088STQ5*PLUS #2: 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: 2.25 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M SPG pH9, 20% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→38.57 Å / Num. all: 15329 / Num. obs: 15329 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 21.95 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.97 / Net I/σ(I): 16.1 / Scaling rejects: 858 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.5→38.57 Å / FOM work R set: 0.8068 / SU ML: 0.29 / σ(F): 1.44 / Phase error: 25.79 / 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 max: 91.09 Å2 / Biso mean: 14.34 Å2 / Biso min: 1.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→38.57 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: 5
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