+Open data
-Basic information
Entry | Database: PDB / ID: 6igu | ||||||
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Title | Crystal structure of the hydrolytic antibody Fab 9C10 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Catalytic Antibody / Hydrolytic Antibody / 9C10 / Fab / ANTIBIOTIC | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TRIETHYLENE GLYCOL Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Yamaguchi, A. / Tada, T. / Tsuchiya, Y. / Tsumuraya, T. / Fujii, I. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the complex of the hydrolytic antibody Fab 9C10 and a transition-state analog Authors: Tsuchiya, Y. / Tada, T. / Yamaguchi, A. / Kumon, A. / Tsumuraya, T. / Fujii, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6igu.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6igu.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 6igu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/6igu ftp://data.pdbj.org/pub/pdb/validation_reports/ig/6igu | HTTPS FTP |
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-Related structure data
Related structure data | 2dtmS 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
#1: Antibody | Mass: 24131.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) | ||||
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#2: Antibody | Mass: 23922.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) | ||||
#3: Chemical | #4: Chemical | #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: 2.56 Å3/Da / Density % sol: 51.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG MME 550, 0.05M calcium chloride, 0.1M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 27974 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rpim(I) all: 0.047 / Net I/σ(I): 16.88 |
Reflection shell | Resolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2.32 / Num. unique obs: 1395 / Rpim(I) all: 0.344 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DTM Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.018 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.187 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.709 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→50 Å
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Refine LS restraints |
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