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Yorodumi- PDB-4xcc: Crystal structure of human 4E10 Fab crystalized in the presence o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xcc | ||||||
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Title | Crystal structure of human 4E10 Fab crystalized in the presence of Phosphatidylcholine (06:0 PC); I422 space group | ||||||
Components |
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Keywords | IMMUNE SYSTEM / 4E10 Fab anti HIV-1 gp41 / lipid membrane / Phosphatidylcholine | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 | 4xcc.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xcc.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xcc ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xcc | HTTPS FTP |
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-Related structure data
Related structure data | 4xawC 4xbeC 4xbgC 4xbpC 4xc1C 4xc3C 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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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23395.850 Da / Num. of mol.: 1 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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#2: Antibody | Mass: 24180.250 Da / Num. of mol.: 1 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-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: Sitting drops contain 4E10 Fab at 10 mg/ml, 10 mM Phosphatidylcholine (06:0 PC) sample mixed (1:1 v/v) with a reservoir solution of 0.2 M di-sodium tartrate, 20% PEG 3350 |
-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: Jul 27, 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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→46.781 Å / Num. obs: 12759 / % possible obs: 92.1 % / Redundancy: 8.6 % / Biso Wilson estimate: 75.4 Å2 / Rsym value: 0.085 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.81→2.86 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 5.3 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FX7 Resolution: 2.81→46.781 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.04 / 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: 73.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→46.781 Å
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Refine LS restraints |
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LS refinement shell |
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