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Yorodumi- PDB-4xcy: Crystal structure of human 4E10 Fab in complex with phosphatidylg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xcy | ||||||
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Title | Crystal structure of human 4E10 Fab in complex with phosphatidylglycerol (06:0 PG) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / 4E10 Fab anti HIV-1 gp41 MPER / membrane lipids / phosphatidylglycerol | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-44G / Unknown ligand Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.96 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 | 4xcy.cif.gz | 436.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xcy.ent.gz | 359.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xcy_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4xcy_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4xcy_validation.xml.gz | 87.1 KB | Display | |
Data in CIF | 4xcy_validation.cif.gz | 117.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xcy ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xcy | HTTPS FTP |
-Related structure data
Related structure data | 4xawC 4xbeC 4xbgC 4xbpC 4xc1C 4xc3C 4xccC 4xceC 4xcfC 4xcnC 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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5 |
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6 |
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Unit cell |
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-Components
#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) #3: Chemical | ChemComp-UNL / Num. of mol.: 5 / Source method: obtained synthetically #4: Chemical | #5: Chemical | ChemComp-GOL / | Nonpolymer details | FIVE UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ...FIVE 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: 2.79 Å3/Da / Density % sol: 55.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: DROP CONTAINS 10 MG/ML 4E10 FAB, 10 MM PHOSPHATIDYLGLYCEROL (06:0 PG) MIXED 1:1 V/V WITH RESERVOIR SOLUTION OF 0.2 M SODIUM IODIDE, 20% PEG 3350, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2013 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.96→48.907 Å / Num. obs: 27268 / % possible obs: 95.5 % / Redundancy: 4.43 % / Biso Wilson estimate: 62.9 Å2 / Rsym value: 0.303 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.96→4.06 Å / Redundancy: 4.16 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.1 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FX7 Resolution: 3.96→48.907 Å / SU ML: 1.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.77 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.8 Å2
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Refinement step | Cycle: LAST / Resolution: 3.96→48.907 Å
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Refine LS restraints |
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LS refinement shell |
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