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Yorodumi- PDB-3g3a: Structure of a lamprey variable lymphocyte receptor in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g3a | ||||||
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Title | Structure of a lamprey variable lymphocyte receptor 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 Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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: 2.2 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 | 3g3a.cif.gz | 234.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g3a.ent.gz | 191.5 KB | Display | PDB format |
PDBx/mmJSON format | 3g3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/3g3a ftp://data.pdbj.org/pub/pdb/validation_reports/g3/3g3a | HTTPS FTP |
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-Related structure data
Related structure data | 3g39SC 3g3bC 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19363.932 Da / Num. of mol.: 4 / 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: D0VX18*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: 3.35 Å3/Da / Density % sol: 63.32 % |
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Crystal grow | Temperature: 296 K / Method: evaporation / pH: 5.6 Details: 2.0 M ammonium sulfate and 0.1 M sodium citrate, pH 5.6, 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: 2.2→50 Å / Num. obs: 88576 / Redundancy: 4.3 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5760 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G39 Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / SU B: 5.931 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.205 / 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: 26.014 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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