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- PDB-4xcn: Crystal structure of human 4E10 Fab in complex with phosphatidic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xcn | ||||||
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Title | Crystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA); 2.9 A resolution | ||||||
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![]() | IMMUNE SYSTEM / human anti gp41 HIV-1 4E10 Fab / membrane lipids / phosphatidic acid | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / PHOSPHATE ION / Unknown ligand![]() | ||||||
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 | ![]() | 504.1 KB | Display | ![]() |
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PDB format | ![]() | 411.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 940.8 KB | Display | ![]() |
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Full document | ![]() | 958.2 KB | Display | |
Data in XML | ![]() | 92.7 KB | Display | |
Data in CIF | ![]() | 129.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xawC ![]() 4xbeC ![]() 4xbgC ![]() 4xbpC ![]() 4xc1C ![]() 4xc3C ![]() 4xccC ![]() 4xceC ![]() 4xcfC ![]() 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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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.) ![]() ![]() #2: Antibody | Mass: 24180.250 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 642 molecules ![](data/chem/img/44E.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-UNL / Num. of mol.: 6 / Source method: obtained synthetically #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: Drop contains 10 mg/ml 4E10 Fab, 10 mM 06:0 PA mixed 1:1 v/v with a reservoir solution of 0.2 M potassium formate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→49.063 Å / Num. obs: 68834 / % possible obs: 98.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.244 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 3.2 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2FX7 Resolution: 2.9→49.063 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.11 / 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: 34.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.063 Å
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Refine LS restraints |
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LS refinement shell |
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