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- PDB-5ifa: Crystal structure of unbound VRC01c-HuGL2 Fab from an HIV-1 naive... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ifa | ||||||
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Title | Crystal structure of unbound VRC01c-HuGL2 Fab from an HIV-1 naive donor at 1.82 A | ||||||
![]() | (VRC01c-HuGL2 Fab ...) x 2 | ||||||
![]() | IMMUNE SYSTEM / VRC01-class naive human germline antibody / CD4 binding site / anti-HIV-1 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sarkar, A. / Wilson, I.A. | ||||||
![]() | ![]() Title: HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen. Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / ...Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / Georgeson, E. / Adachi, Y. / Kubitz, M. / deCamp, A.C. / Julien, J.P. / Wilson, I.A. / Burton, D.R. / Crotty, S. / Schief, W.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.9 KB | Display | ![]() |
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PDB format | ![]() | 147.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.9 KB | Display | ![]() |
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Full document | ![]() | 471.2 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5idlC ![]() 5iesC ![]() 5if0C ![]() 4jpkS 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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Unit cell |
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Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23614.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23816.408 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 4 types, 217 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-1PE / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M lithium sulfate and 20% (w/v) PEG3350, and cryo-protected with 25% glycerol |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→48.84 Å / Num. obs: 40894 / % possible obs: 97.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.872 / Rsym value: 0.163 / Net I/σ(I): 0.95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JPK Resolution: 1.821→48.837 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.51 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.821→48.837 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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