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Yorodumi- PDB-6w73: Fab Structure of CD4 Binding Site (CD4bs) Huamn Monoclonal Antibo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w73 | |||||||||
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Title | Fab Structure of CD4 Binding Site (CD4bs) Huamn Monoclonal Antibody HmAb64 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 gp120 / antibody / IgG | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Kong, X. / Pan, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: A CD4 Binding Site (CD4bs) Monoclonal Antibody Elicited from A Human Volunteer Immunized by a DNA Prime/Protein Boost gp120 HIV Vaccine Authors: Kong, X. / Pan, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w73.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w73.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 6w73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w73_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 6w73_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 6w73_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 6w73_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w73 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w73 | HTTPS FTP |
-Related structure data
Related structure data | 1deeS 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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Unit cell |
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-Components
#1: Antibody | Mass: 23353.816 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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#2: Antibody | Mass: 24023.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.05 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 30% PEG1500, 8%MPD, 0.1M Tris pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45.63 Å / Num. obs: 21339 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 48.4 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.8→2.97 Å / Mean I/σ(I) obs: 2.84 / Num. unique obs: 1621 / CC1/2: 0.882 / Rrim(I) all: 0.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DEE Resolution: 2.8→45.63 Å / SU ML: 0.4188 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.074
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.63 Å
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Refine LS restraints |
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LS refinement shell |
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