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Yorodumi- PDB-3ke4: Crystal structure of a PduO-Type ATP:Cob(I)alamin adenosyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ke4 | ||||||
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Title | Crystal structure of a PduO-Type ATP:Cob(I)alamin adenosyltransferase from Bacillus cereus | ||||||
Components | Hypothetical Cytosolic Protein | ||||||
Keywords | TRANSFERASE / Helix bundle | ||||||
Function / homology | Function and homology information corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / cobalamin biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Park, A.K. / Moon, J.H. / Chi, Y.M. | ||||||
Citation | Journal: To be Published Title: Crystal structure of a PduO-Type ATP:Cob(I)alamin adenosyltransferase from Bacillus cereus Authors: Park, A.K. / Moon, J.H. / Chi, Y.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ke4.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ke4.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ke4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/3ke4 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/3ke4 | HTTPS FTP |
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-Related structure data
Related structure data | 2ah6S 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
#1: Protein | Mass: 23936.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q813T7, corrinoid adenosyltransferase #2: Chemical | ChemComp-DIO / #3: 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: 2.46 Å3/Da / Density % sol: 49.93 % / Mosaicity: 0.224 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH 6.5, 1.52M ammonium sulfate, 9%(v/v) dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23986 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 29, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.23986 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 53001 / % possible obs: 94.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Χ2: 0.801 / Net I/σ(I): 14.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ah6 Resolution: 1.9→39.64 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
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Solvent computation | Bsol: 58.322 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.4 Å2 / Biso mean: 24.478 Å2 / Biso min: 2.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→39.64 Å
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Refine LS restraints |
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Xplor file |
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