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Yorodumi- PDB-2o5z: Crystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab 5-beta-andr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o5z | ||||||
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Title | Crystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab 5-beta-androstane-3,17-dione complex | ||||||
Components | (chimeric antibody Fab 1E9-DB3) x 2 | ||||||
Keywords | IMMUNE SYSTEM / immunoglobulin / chimeric Fab / antibody engineering / evolution of ligand recognition | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 5-BETA-ANDROSTANE-3,17-DIONE Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 2.4 Å | ||||||
Authors | Verdino, P. / Wilson, I.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Closely related antibody receptors exploit fundamentally different strategies for steroid recognition. Authors: Verdino, P. / Aldag, C. / Hilvert, D. / 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 | 2o5z.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o5z.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 2o5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/2o5z ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o5z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 24143.002 Da / Num. of mol.: 1 / Fragment: light chain / Mutation: G63S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-1E9 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 | ||||
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#2: Antibody | Mass: 24425.525 Da / Num. of mol.: 1 / Fragment: heavy chain / Mutation: L47W, M87T, R100W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-1E9 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ANO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2.0 M ammonium sulfate, 0.15 M sodium citrate, 0.01% PEG 20000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.05966 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05966 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 33879 / Num. obs: 33845 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 8.5 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.7 / Rsym value: 52.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.7 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.053 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.464 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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