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Yorodumi- PDB-2ak1: Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ak1 | ||||||
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Title | Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with benzoic acid | ||||||
Components | (Antibody 7A1 Fab') x 2 | ||||||
Keywords | IMMUNE SYSTEM / catalytic Antibody / Fab / benzoic acid / HYDROLYTIC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 2ak1.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ak1.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ak1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/2ak1 ftp://data.pdbj.org/pub/pdb/validation_reports/ak/2ak1 | HTTPS FTP |
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-Related structure data
Related structure data | 2ajsSC 2ajuC 2ajvC 2ajxC 2ajyC 2ajzC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#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 | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-BEZ / | #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: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 4000, zinc acetate, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 22, 2003 |
Radiation | Monochromator: DOUBLE-CRYSTAL, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 48913 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.058 / Χ2: 1.541 |
Reflection shell | Resolution: 1.85→1.89 Å / % possible obs: 97.9 % / Rmerge(I) obs: 0.571 / Num. measured obs: 3166 / Χ2: 0.628 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AJS Resolution: 1.85→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 43.458 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.095 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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