+Open data
-Basic information
Entry | Database: PDB / ID: 6n32 | |||||||||
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Title | Anti-HIV-1 Fab 2G12 re-refinement | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / carbohydrate / HIV-1 | |||||||||
Function / homology | Function and homology information immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Calarese, D.A. / Stanfield, R.L. / Wilson, I.A. | |||||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n32.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n32.ent.gz | 142.2 KB | Display | PDB format |
PDBx/mmJSON format | 6n32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/6n32 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/6n32 | HTTPS FTP |
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-Related structure data
Related structure data | 6n2xC 6n35C 1fvdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX7 #2: Antibody | Mass: 23932.869 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: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.05M ammonium sulfate, 18% Peg 6000, 0.1M imidazole malate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9759 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9759 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→18.739 Å / Num. obs: 59743 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2672 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FVD Resolution: 2.2→18.739 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→18.739 Å
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Refine LS restraints |
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LS refinement shell |
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