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Yorodumi- PDB-3f12: Germline V-genes sculpt the binding site of a family of antibodie... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f12 | ||||||
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Title | Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Human cytomegalovirus / antibody / germline / Immunoglobulin domain | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 | 3f12.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f12.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f12_validation.pdf.gz | 450.1 KB | Display | wwPDB validaton report |
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Full document | 3f12_full_validation.pdf.gz | 512 KB | Display | |
Data in XML | 3f12_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3f12_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/3f12 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/3f12 | HTTPS FTP |
-Related structure data
Related structure data | 3eyfC 3eyoSC 3eyqC 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23723.350 Da / Num. of mol.: 2 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 #2: Antibody | Mass: 25842.934 Da / Num. of mol.: 2 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 |
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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: 2.72 Å3/Da / Density % sol: 54.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.6 Details: 2.6 M Ammonium sulfate, 2% PEG 400 in 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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. all: 23047 / Num. obs: 23047 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.12 |
Reflection shell | Resolution: 2.95→3.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 3.84 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EYO Resolution: 2.95→50 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.8 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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Refine LS restraints |
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