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Yorodumi- PDB-3o2w: Crystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o2w | ||||||
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Title | Crystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab in complex with a 39A11 transition state analog | ||||||
Components | (Chimeric antibody Fab 1E9, ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / IgG antibody Fab | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION / Chem-O2W Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 2.55 Å | ||||||
Authors | Verdino, P. / Wilson, I.A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab in complex with a 39A11 transition state analog 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 | 3o2w.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o2w.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 3o2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o2w_validation.pdf.gz | 784.6 KB | Display | wwPDB validaton report |
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Full document | 3o2w_full_validation.pdf.gz | 792.5 KB | Display | |
Data in XML | 3o2w_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 3o2w_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/3o2w ftp://data.pdbj.org/pub/pdb/validation_reports/o2/3o2w | HTTPS FTP |
-Related structure data
Related structure data | |
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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
-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 , 5 types, 88 molecules
#3: Chemical | ChemComp-O2W / | ||||||
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#4: Chemical | ChemComp-TRS / #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: 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: 4.51 Å3/Da / Density % sol: 72.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.25M ammoniumsulfate, 0.15M sodiumcitrate, 0.01% PEG20000, pH 8.5, 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: 1.059658 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: 1.059658 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 28353 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.071 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.55→2.64 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.55 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement Starting model: 1E9 PheL89Ser/LeuH47Trp/MetH100bPhe Fab apo structure Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.48 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R Free: 0.238 / 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: 79.982 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.552→2.618 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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