+Open data
-Basic information
Entry | Database: PDB / ID: 2ymx | ||||||
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Title | Crystal structure of inhibitory anti-AChE Fab408 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ACETYLCHOLINESTERASE / INHIBITION / BACK DOOR REGION | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bourne, Y. / Renault, L. / Essono, S. / Mondielli, G. / Lamourette, P. / Bocquet, D. / Grassi, J. / Marchot, P. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Molecular Characterization of Monoclonal Antibodies that Inhibit Acetylcholinesterase by Targeting the Peripheral Site and Backdoor Region Authors: Bourne, Y. / Renault, L. / Essono, S. / Mondielli, G. / Lamourette, P. / Boquet, D. / Grassi, J. / Marchot, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ymx.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ymx.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ymx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/2ymx ftp://data.pdbj.org/pub/pdb/validation_reports/ym/2ymx | HTTPS FTP |
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-Related 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: 24132.043 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) |
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#2: Antibody | Mass: 23574.840 Da / Num. of mol.: 1 / Fragment: VARIABLE DOMAIN / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.38 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 6 / Details: 18% PEG 6000, 100 MM SODIUM CACODYLATE PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 35565 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.8 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1FGV AND 1WEJ Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.748 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 42.697 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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