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Yorodumi- PDB-3o2v: Crystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o2v | ||||||
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Title | Crystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engineered Diels-Alderase Fab with modified specificity and catalytic activity | ||||||
Components | (Chimeric antibody Fab 1E9, ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / IgG antibody Fab | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Verdino, P. / Wilson, I.A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe, an engineered Diels-Alderase Fab with modified specificity and catalytic activity Authors: Verdino, P. / Aldag, C. / Jonsson, S. / 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 | 3o2v.cif.gz | 196.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o2v.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 3o2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/3o2v ftp://data.pdbj.org/pub/pdb/validation_reports/o2/3o2v | HTTPS FTP |
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-Related structure data
Related structure data | 2o5xS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 24082.904 Da / Num. of mol.: 1 / Mutation: F89S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-1E9(PheL89Ser/LeuH47Trp/MetH100bPhe) / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 |
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#2: Antibody | Mass: 24428.510 Da / Num. of mol.: 1 / Mutation: L47T, M100bF Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: p4xH-1E9(PheL89Ser/LeuH47Trp/MetH100bPhe) / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 |
-Non-polymers , 4 types, 188 molecules
#3: Chemical | ChemComp-TRS / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: 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: 4.55 Å3/Da / Density % sol: 72.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.75M ammoniumsulfate, 0.15M sodiumcitrate, 0.01% PEG20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Date: Jul 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 39314 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.057 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.557 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O5X Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 10.581 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R Free: 0.163 / 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: 52.729 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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