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Yorodumi- PDB-8sm1: CRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sm1 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN-BARR VIRUS MAJOR GLYCOPROTEIN GP350 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human herpesvirus 4 (Epstein-Barr virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å | ||||||
Authors | Chen, W.-H. / Bu, W. / Cohen, J.I. / Kanekiyo, M. / Joyce, M.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structural Basis For Receptor Engagement And Virus Neutralization Through Epstein-Barr Virus Gp350 Authors: Chen, W.-H. / Bu, W. / Cohen, J.I. / Kanekiyo, M. / Joyce, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sm1.cif.gz | 338.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sm1.ent.gz | 276.4 KB | Display | PDB format |
PDBx/mmJSON format | 8sm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/8sm1 ftp://data.pdbj.org/pub/pdb/validation_reports/sm/8sm1 | HTTPS FTP |
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-Related structure data
Related structure data | 8sm0C 2h6oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24115.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23435.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 9 molecules G
#1: Protein | Mass: 46895.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus) Strain: B95-8 / Gene: BLLF1 / Production host: Homo sapiens (human) / References: UniProt: P03200 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 2 molecules
#5: Chemical | ChemComp-GOL / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 3.03 Å3/Da / Density % sol: 59.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.60M AMMONIUM SULFATE, 2% PEG 400, 0.5% GLYCEROL, 0.1M SODIUM ACETATE PH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.285→50 Å / Num. obs: 16984 / % possible obs: 83 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.09 |
Reflection shell | Resolution: 3.3→3.42 Å / Rmerge(I) obs: 0.703 / Num. unique obs: 1486 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H6O Resolution: 3.29→45.78 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.29→45.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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