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Yorodumi- PDB-3eyq: Crystal structure of MJ5 Fab, a germline antibody variant of anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eyq | ||||||
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Title | Crystal structure of MJ5 Fab, a germline antibody variant of anti-human cytomegalovirus antibody 8f9 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Human cytomegalovirus / antibody / Immunoglobulin domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Thomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus. Authors: Thomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eyq.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eyq.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 3eyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eyq_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 3eyq_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 3eyq_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 3eyq_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3eyq ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eyq | HTTPS FTP |
-Related structure data
Related structure data | 3eyfSC 3eyoC 3f12C 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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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23692.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6PIL8*PLUS |
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#2: Antibody | Mass: 25828.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q0ZCI9*PLUS |
#3: 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: 2.8 Å3/Da / Density % sol: 56.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.6 Details: 2.6M Ammonium sulfate, 2% PEG 400, 0.1M CAPS buffer, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 13, 2006 |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 19825 / Num. obs: 19825 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.41 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EYF Resolution: 2.4→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.3 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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