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Yorodumi- PDB-3w9e: Structure of Human Monoclonal Antibody E317 Fab Complex with HSV-2 gD -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w9e | |||||||||
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Title | Structure of Human Monoclonal Antibody E317 Fab Complex with HSV-2 gD | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / IgG fold / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / symbiont entry into host cell / viral envelope / virion membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Human herpesvirus 2 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Lee, C.C. / Lin, L.L. / Wang, A.H.J. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural basis for the antibody neutralization of herpes simplex virus Authors: Lee, C.C. / Lin, L.L. / Chan, W.E. / Ko, T.P. / Lai, J.S. / Wang, A.H.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w9e.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w9e.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 3w9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/3w9e ftp://data.pdbj.org/pub/pdb/validation_reports/w9/3w9e | HTTPS FTP |
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-Related structure data
Related structure data | 3w9dSC 1l2gS 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
-Antibody , 2 types, 2 molecules AB
#2: Antibody | Mass: 23618.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTCAE8 / Cell (production host): Mammalian cell / Cell line (production host): PER.C6 / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23133.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTCAE8 / Cell (production host): Mammalian cell / Cell line (production host): PER.C6 / Production host: Homo sapiens (human) |
-Protein / Non-polymers , 2 types, 253 molecules C
#1: Protein | Mass: 34138.055 Da / Num. of mol.: 1 / Fragment: UNP residues 1-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 2 / Strain: HG52 / Gene: gD / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q69467 |
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#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8.2 Details: 30%(v/v) PEG 550MME, 0.1M Na HEPES, pH 8.2, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 38408 / Num. obs: 37832 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 26.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1L2G, 3W9D Resolution: 2.3→29.78 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.353 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 52.342 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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