[English] 日本語
Yorodumi- PDB-3idm: Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3idm | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 Fab' fragment in complex with gp41 Peptide analog ELD(Nrg)WAS | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / HIV-1 / gp41 / MPER / 2F5 | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | |||||||||
Authors | Julien, J.-P. / Bryson, S. / Pai, E.F. | |||||||||
Citation | Journal: J.Virol. / Year: 2009 Title: Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications. Authors: Bryson, S. / Julien, J.P. / Hynes, R.C. / Pai, E.F. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3idm.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3idm.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 3idm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/3idm ftp://data.pdbj.org/pub/pdb/validation_reports/id/3idm | HTTPS FTP |
---|
-Related structure data
Related structure data | 1u8hC 1u8iC 1u8jC 1u8lC 1u8mC 1u8nC 1u8oC 1u8pC 1u8qC 1u91C 1u92C 1u93C 1u95C 2f5aC 2f5bC 2pw1C 2pw2C 3idgC 3idiC 3idjC 3idnC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
---|---|
#2: Antibody | Mass: 25245.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#3: Protein/peptide | Mass: 920.924 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.59 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M sodium acetate, pH 5.6, 1.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 14, 2005 |
Radiation | Monochromator: Xenocs optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→80 Å / Num. all: 33120 / Num. obs: 30834 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.3 Å2 / Rsym value: 0.66 |
Reflection shell | Resolution: 2.24→2.38 Å / Rsym value: 0.385 / % possible all: 92.7 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→60.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 885298.4 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.7883 Å2 / ksol: 0.356744 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→60.89 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.24→2.38 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|