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Yorodumi- PDB-2ajs: Crystal structure of cocaine catalytic antibody 7A1 Fab' in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ajs | ||||||
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Title | Crystal structure of cocaine catalytic antibody 7A1 Fab' in complex with heptaethylene glycol | ||||||
Components | (Antibody 7A1 ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / CATALYTIC Antibody / Fab / COCAINE / HYDROLYTIC / Heptaethylene glycol | ||||||
Function / homology | Function and homology information IgG immunoglobulin complex / B cell differentiation / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Zhu, X. / Wilson, I.A. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Complete reaction cycle of a cocaine catalytic antibody at atomic resolution. Authors: Zhu, X. / Dickerson, T.J. / Rogers, C.J. / Kaufmann, G.F. / Mee, J.M. / McKenzie, K.M. / Janda, K.D. / Wilson, I.A. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of these proteins are not available at any sequence database at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ajs.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ajs.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ajs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/2ajs ftp://data.pdbj.org/pub/pdb/validation_reports/aj/2ajs | HTTPS FTP |
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-Related structure data
Related structure data | 2ajuC 2ajvC 2ajxC 2ajyC 2ajzC 2ak1C 1cloS 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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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 24059.611 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN IGG1 kappa light chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS |
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#2: Antibody | Mass: 23865.783 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN IGG1 HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5M842*PLUS |
-Non-polymers , 4 types, 411 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-P33 / | #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: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 400, ammonium sulfate, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.983969 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.983969 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 59095 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.057 / Χ2: 1.401 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1CLO Resolution: 1.7→22.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.431 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 30.306 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→22.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.745 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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