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- PDB-4xce: Crystal structure of human 4E10 Fab crystalized in the presence o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xce | ||||||
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Title | Crystal structure of human 4E10 Fab crystalized in the presence of Phosphatidylcholine (06:0 PC); C2 space group | ||||||
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![]() | IMMUNE SYSTEM / 4E10 Fab anti HIV-1 gp41 / Phosphatidylcholine / membrane lipid | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Irimia, A. / Stanfield, R.L. / Wilson, I.A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.4 KB | Display | ![]() |
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PDB format | ![]() | 201.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4xawC ![]() 4xbeC ![]() 4xbgC ![]() 4xbpC ![]() 4xc1C ![]() 4xc3C ![]() 4xccC ![]() 4xcfC ![]() 4xcnC ![]() 4xcyC ![]() 2fx7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23395.850 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 24180.250 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: Sitting drops contain 4E10 Fab at 10 mg/ml, 10 mM Phosphatidylcholine (06:0 PC) sample mixed (1:1 v/v) with reservoir solution of 0.2 M potassium sodium tartrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.93→46.995 Å / Num. obs: 31840 / % possible obs: 94.2 % / Redundancy: 2.7 % / Biso Wilson estimate: 63.2 Å2 / Rsym value: 0.089 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.93→2.98 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.2 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2FX7 Resolution: 2.93→46.995 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.04 / 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: 72.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.93→46.995 Å
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Refine LS restraints |
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LS refinement shell |
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