[English] 日本語
Yorodumi- PDB-2i9l: Structure of Fab 7D11 from a neutralizing antibody against the po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i9l | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Fab 7D11 from a neutralizing antibody against the poxvirus L1 protein | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / Neutralizing antibody / Poxvirus / antibody complex / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Vaccinia virus Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Su, H.P. / Golden, J.W. / Gittis, A.G. / Moss, B. / Hooper, J.W. / Garboczi, D.N. | ||||||
Citation | Journal: Virology / Year: 2007 Title: Structural basis for the binding of the neutralizing antibody, 7D11, to the poxvirus L1 protein Authors: Su, H.-P. / Golden, J.W. / Gittis, A.G. / Hooper, J.W. / Garboczi, D.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2i9l.cif.gz | 459.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2i9l.ent.gz | 377.6 KB | Display | PDB format |
PDBx/mmJSON format | 2i9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/2i9l ftp://data.pdbj.org/pub/pdb/validation_reports/i9/2i9l | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 24175.852 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Antibody light chain isolated from a hybridoma / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 23668.525 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Antibody heavy chain isolated from a hybridoma / Source: (natural) Mus musculus (house mouse) #3: Protein | Mass: 19532.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: Western Reserve / Gene: l1r / Plasmid: pNAN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) - RIL / References: UniProt: P07612 #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 8 Details: 10% PEG 10000, 0.1M Tris, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2005 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 61289 / % possible obs: 98.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.464 / % possible all: 99.6 |
-Phasing
Phasing MR |
|
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YPY, 1YMH Resolution: 3.1→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 10 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1→3.12 Å / Total num. of bins used: 50 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|