+Open data
-Basic information
Entry | Database: PDB / ID: 4b50 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the HIV-1 gp41 MPER-specific llama VHH 2H10 | ||||||
Components | 2H10 LLAMA VHH | ||||||
Keywords | IMMUNE SYSTEM / NEUTRALIZING ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | LAMA GLAMA (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Lutje Hulsik, D. / Sabin, C. / Macheboeuf, P. / Weissenhorn, W. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013 Title: A Gp41 Mper-Specific Llama Vhh Requires a Hydrophobic Cdr3 for Neutralization But not for Antigen Recognition. Authors: Lutje Hulsik, D. / Liu, Y.Y. / Strokappe, N.M. / Battella, S. / El Khattabi, M. / Mccoy, L.E. / Sabin, C. / Hinz, A. / Hock, M. / Macheboeuf, P. / Bonvin, A.M. / Langedijk, J.P. / Davis, D. ...Authors: Lutje Hulsik, D. / Liu, Y.Y. / Strokappe, N.M. / Battella, S. / El Khattabi, M. / Mccoy, L.E. / Sabin, C. / Hinz, A. / Hock, M. / Macheboeuf, P. / Bonvin, A.M. / Langedijk, J.P. / Davis, D. / Forsman Quigley, A. / Aasa-Chapman, M.M. / Seaman, M.S. / Ramos, A. / Poignard, P. / Favier, A. / Simorre, J.P. / Weiss, R.A. / Verrips, C.T. / Weissenhorn, W. / Rutten, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4b50.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4b50.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 4b50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/4b50 ftp://data.pdbj.org/pub/pdb/validation_reports/b5/4b50 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ezjS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 13351.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44 % / Description: NONE |
---|---|
Crystal grow | pH: 9 / Details: 0.1 M BICINE, 3.2 M (NH4)2SO4, PH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→25 Å / Num. obs: 28043 / % possible obs: 99 % / Observed criterion σ(I): 2.2 / Redundancy: 13.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EZJ Resolution: 1.3→63.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.105 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→63.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|