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Yorodumi- PDB-3g3b: Structure of a lamprey variable lymphocyte receptor mutant in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g3b | ||||||
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Title | Structure of a lamprey variable lymphocyte receptor mutant in complex with a protein antigen | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / VLR / antibody / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Hydrolase / HYDROLASE-IMMUNE SYSTEM COMPLEX | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Petromyzon marinus (sea lamprey) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 3g3b.cif.gz | 213.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g3b.ent.gz | 172.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g3b_validation.pdf.gz | 483.4 KB | Display | wwPDB validaton report |
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Full document | 3g3b_full_validation.pdf.gz | 503.6 KB | Display | |
Data in XML | 3g3b_validation.xml.gz | 40 KB | Display | |
Data in CIF | 3g3b_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/3g3b ftp://data.pdbj.org/pub/pdb/validation_reports/g3/3g3b | HTTPS FTP |
-Related structure data
Related structure data | 3g39C 3g3aSC 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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Unit cell |
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-Components
#1: Protein | Mass: 18720.240 Da / Num. of mol.: 4 / Fragment: variable lymphocyte receptor 2D13 / Mutation: Q40R, K101R, G132W, P142H, E159K 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: D0VX19*PLUS #2: Protein | Mass: 14331.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Strain: Chicken / Gene: lysozyme, LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme #3: 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: 2.76 Å3/Da / Density % sol: 55.44 % |
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Crystal grow | Temperature: 296 K / Method: evaporation / pH: 8.5 Details: 8% (w/v) polyethylene glycol 8000, 0.1 M Tris-HCl, pH 8.5, 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: 2.4→30 Å / Num. obs: 60645 / Redundancy: 13.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 14 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 6.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G3A Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.899 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.274 / 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: 44.722 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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