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Open data
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Basic information
Entry | Database: PDB / ID: 6n2x | ||||||||||||
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Title | Anti-HIV-1 Fab 2G12 + Man9 re-refinement | ||||||||||||
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![]() | IMMUNE SYSTEM / antibody / carbohydrate / HIV-1 | ||||||||||||
Function / homology | ![]() 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 | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Calarese, D.A. / Stanfield, R.L. / Wilson, I.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.3 KB | Display | ![]() |
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PDB format | ![]() | 145.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 31 KB | Display | |
Data in CIF | ![]() | 42.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n32C ![]() 6n35C ![]() 1op3 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23245.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 23845.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68.48 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→43.3 Å
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Refine LS restraints |
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LS refinement shell |
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