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Yorodumi- PDB-2o5x: Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o5x | ||||||
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Title | Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM steroid-binding affinity | ||||||
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 Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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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Remark 999 | SEQUENCE There is no aminoacid sequence database reference available for the protein. The protein ...SEQUENCE There is no aminoacid sequence database reference available for the protein. The protein was designed using variable domains from mouse and the constant domains from humans |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o5x.cif.gz | 111.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o5x.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 2o5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/2o5x ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o5x | HTTPS FTP |
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-Related structure data
Related structure data | 2o5yC 2o5zC 1c1eS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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-TRS / | #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: 4.54 Å3/Da / Density % sol: 72.89 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.5 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: 0.99996 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99996 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 54755 / Num. obs: 54536 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 8.2 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.05→2.29 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.4 / Rsym value: 52.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1C1E Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.275 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.637 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 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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