+Open data
-Basic information
Entry | Database: PDB / ID: 6n2x | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Anti-HIV-1 Fab 2G12 + Man9 re-refinement | ||||||||||||
Components |
| ||||||||||||
Keywords | IMMUNE SYSTEM / antibody / carbohydrate / HIV-1 | ||||||||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||||||||
Authors | Calarese, D.A. / Stanfield, R.L. / Wilson, I.A. | ||||||||||||
Funding support | United States, 1items
| ||||||||||||
Citation | Journal: Science / Year: 2003 Title: Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Authors: Calarese, D.A. / Scanlan, C.N. / Zwick, M.B. / Deechongkit, S. / Mimura, Y. / Kunert, R. / Zhu, P. / Wormald, M.R. / Stanfield, R.L. / Roux, K.H. / Kelly, J.W. / Rudd, P.M. / Dwek, R.A. / ...Authors: Calarese, D.A. / Scanlan, C.N. / Zwick, M.B. / Deechongkit, S. / Mimura, Y. / Kunert, R. / Zhu, P. / Wormald, M.R. / Stanfield, R.L. / Roux, K.H. / Kelly, J.W. / Rudd, P.M. / Dwek, R.A. / Katinger, H. / Burton, D.R. / Wilson, I.A. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6n2x.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6n2x.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 6n2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n2x_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6n2x_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6n2x_validation.xml.gz | 31 KB | Display | |
Data in CIF | 6n2x_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/6n2x ftp://data.pdbj.org/pub/pdb/validation_reports/n2/6n2x | HTTPS FTP |
-Related structure data
Related structure data | 6n32C 6n35C 1op3 S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23245.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX7 #2: Antibody | Mass: 23845.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5 #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.48 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% Peg 400, 0.2M imidazole malate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.984 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 3→43.3 Å / Num. obs: 29134 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 75.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1346 / % possible all: 89.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OP3 1op3 Resolution: 3→43.3 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.96
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→43.3 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|