+Open data
-Basic information
Entry | Database: PDB / ID: 3m19 | ||||||
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Title | Crystal structure of variable lymphocyte receptor VLRA.R5.1 | ||||||
Components | Variable lymphocyte receptor A diversity region | ||||||
Keywords | IMMUNE SYSTEM / variable lymphocyte receptor / adaptive immunity / antibody / T cell / B cell / leucine-rich repeat | ||||||
Function / homology | Function and homology information Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Petromyzon marinus (sea lamprey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Deng, L. / Velikovsky, C.A. / Mariuzza, R.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey. Authors: Deng, L. / Velikovsky, C.A. / Xu, G. / Iyer, L.M. / Tasumi, S. / Kerzic, M.C. / Flajnik, M.F. / Aravind, L. / Pancer, Z. / 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 | 3m19.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m19.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 3m19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/3m19 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/3m19 | HTTPS FTP |
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-Related structure data
Related structure data | 3m18SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27477.963 Da / Num. of mol.: 2 / Fragment: Ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Gene: VLRA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3) / References: UniProt: C7B6Z3 #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: 2.15 Å3/Da / Density % sol: 42.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% (w/v) polyethylene glycol 6000, 1.0 M LiCl and 0.1 M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 48278 / Redundancy: 3.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.7→1.82 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3M18 Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.523 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.207 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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