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- PDB-5tfw: Crystal structure of 10E8 Fab light chain mutant2 against the MPE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5tfw | |||||||||
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Title | Crystal structure of 10E8 Fab light chain mutant2 against the MPER region of the HIV-1 Env, in complex with T117v2 epitope scaffold | |||||||||
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![]() | IMMUNE SYSTEM / HIV-1 GP41 MPER / 10E8 FAB / LIPID MEMBRANE | |||||||||
Function / homology | Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / DI(HYDROXYETHYL)ETHER![]() | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Irimia, A. / Wilson, I.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design. Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / ...Authors: Irimia, A. / Serra, A.M. / Sarkar, A. / Jacak, R. / Kalyuzhniy, O. / Sok, D. / Saye-Francisco, K.L. / Schiffner, T. / Tingle, R. / Kubitz, M. / Adachi, Y. / Stanfield, R.L. / Deller, M.C. / Burton, D.R. / Schief, W.R. / 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 | ![]() | 253.2 KB | Display | ![]() |
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PDB format | ![]() | 202.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5sy8C ![]() 5t29C ![]() 5t5bC ![]() 5t6lC ![]() 5t80C ![]() 5t85C ![]() 3lf6S ![]() 4g6fS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules O
#3: Protein | Mass: 18643.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: PET29 / Production host: ![]() ![]() |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 25447.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 22863.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 3 types, 233 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PEG / |
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#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.8 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion / pH: 6.9 Details: 0.2 M Na thiocyanate, 20% PEG 3350, pH 6.9, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.168→47.235 Å / Num. obs: 36138 / % possible obs: 94.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 41 Å2 / CC1/2: 0.999 / Rsym value: 0.056 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.168→2.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.835 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4G6F, 3LF6 Resolution: 2.168→47.235 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.77 / 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: 59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.168→47.235 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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