+Open data
-Basic information
Entry | Database: PDB / ID: 3g39 | ||||||
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Title | Structure of a lamprey variable lymphocyte receptor | ||||||
Components | Variable lymphocyte receptor VLRB.2D | ||||||
Keywords | IMMUNE SYSTEM / VLR / antibody | ||||||
Function / homology | Function and homology information Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / 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: 1.55 Å | ||||||
Authors | Deng, L. / Velikovsky, C.A. / Mariuzza, R.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen. Authors: Velikovsky, C.A. / Deng, L. / Tasumi, S. / Iyer, L.M. / Kerzic, M.C. / 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 | 3g39.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g39.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 3g39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/3g39 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/3g39 | HTTPS FTP |
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-Related structure data
Related structure data | 3g3aC 3g3bC 2o6sS C: citing same article (ref.) 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: 18492.904 Da / Num. of mol.: 1 / Fragment: Ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Gene: vlr / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: D0VX17*PLUS |
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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: 1.88 Å3/Da / Density % sol: 34.43 % |
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Crystal grow | Temperature: 296 K / Method: evaporation / pH: 7.5 Details: 70% (w/v) 2-methyl-2,4-pentanediol and 0.1 M Hepes, pH 7.5, EVAPORATION, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 19434 / Redundancy: 22.2 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 55.8 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 20 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1908 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O6S Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.368 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 19.684 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.551→1.591 Å / Total num. of bins used: 20
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