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Yorodumi- PDB-4xbg: Crystal structure of human 4E10 Fab in complex with phosphatidic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xbg | ||||||
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Title | Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA): 2.73 A resolution | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human anti gp41 HIV-1 4E10 Fab / membrane lipid / phosphatidic acid | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / PHOSPHATE ION / Unknown ligand Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Irimia, A. / Stanfield, R.L. / Wilson, I.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Immunity / Year: 2016 Title: Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10. Authors: Irimia, A. / Sarkar, A. / Stanfield, R.L. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xbg.cif.gz | 502.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xbg.ent.gz | 412 KB | Display | PDB format |
PDBx/mmJSON format | 4xbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xbg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4xbg_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4xbg_validation.xml.gz | 90.9 KB | Display | |
Data in CIF | 4xbg_validation.cif.gz | 126.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xbg ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xbg | HTTPS FTP |
-Related structure data
Related structure data | 4xawC 4xbeC 4xbpC 4xc1C 4xc3C 4xccC 4xceC 4xcfC 4xcnC 4xcyC 2fx7S 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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2 |
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3 |
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6 |
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Unit cell |
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-Components
-Antibody , 2 types, 12 molecules LBDFIKHACEGJ
#1: Antibody | Mass: 23395.850 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human) #2: Antibody | Mass: 24180.250 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human) |
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-Non-polymers , 5 types, 509 molecules
#3: Chemical | ChemComp-UNL / Num. of mol.: 6 / Source method: obtained synthetically #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PO4 / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | SIX UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ...SIX UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTIO |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: Reservoir: 0.2 M potassium formate, 35% PEG 3350 / PH range: 6.5-7.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2013 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111), non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→39.241 Å / Num. obs: 81191 / % possible obs: 97.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 46.1 Å2 / Rsym value: 0.102 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.73→2.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FX7 Resolution: 2.73→39.241 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.68 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→39.241 Å
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Refine LS restraints |
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LS refinement shell |
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