[English] 日本語
Yorodumi- PDB-4xml: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xml | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424 | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / HIV-1 gp120 / monoclonal antibody | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.68 Å | |||||||||
Authors | Pan, R. / Kong, X.-P. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: J.Virol. / Year: 2015 Title: Functional and Structural Characterization of Human V3-Specific Monoclonal Antibody 2424 with Neutralizing Activity against HIV-1 JRFL. Authors: Kumar, R. / Pan, R. / Upadhyay, C. / Mayr, L. / Cohen, S. / Wang, X.H. / Balasubramanian, P. / Nadas, A. / Seaman, M.S. / Zolla-Pazner, S. / Gorny, M.K. / Kong, X.P. / Hioe, C.E. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xml.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xml.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xml_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4xml_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 4xml_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4xml_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/4xml ftp://data.pdbj.org/pub/pdb/validation_reports/xm/4xml | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23533.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
---|---|
#2: Antibody | Mass: 23696.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 8000, Tris, glycerol / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→50 Å / Num. obs: 13122 / % possible obs: 99.1 % / Redundancy: 3.2 % / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.68→2.84 Å / Mean I/σ(I) obs: 1.98 / % possible all: 98.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.68→47.862 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 30.64 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→47.862 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|