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Yorodumi- PDB-2zhy: Crystal structure of a pduO-type ATP:cobalamin adenosyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zhy | ||||||
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Title | Crystal structure of a pduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis | ||||||
Components | ATP:cob(I)alamin adenosyltransferase, putative | ||||||
Keywords | TRANSFERASE / helix bundle | ||||||
Function / homology | Function and homology information corrinoid adenosyltransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cobalamin biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Burkholderia thailandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Moon, J.H. / Park, A.K. / Jang, E.H. / Kim, H.S. / Chi, Y.M. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of a PduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis. Authors: Moon, J.H. / Park, A.K. / Jang, E.H. / Kim, H.S. / 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 | 2zhy.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zhy.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/2zhy ftp://data.pdbj.org/pub/pdb/validation_reports/zh/2zhy | 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
#1: Protein | Mass: 19522.150 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: pduO / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2SZ09, corrinoid adenosyltransferase #2: 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: 2.63 Å3/Da / Density % sol: 53.29 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 0.1M Na Citrate, 22% Isopropanol, 12% PEG 4000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9999 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 7, 2007 / Details: mirrors |
Radiation | Monochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 54263 / Num. obs: 54261 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 14.7 Å2 / Limit h max: 29 / Limit h min: 0 / Limit k max: 82 / Limit k min: 0 / Limit l max: 86 / Limit l min: 0 / Observed criterion F max: 54211.48 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.091 / Χ2: 1.713 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.344 / Num. unique all: 3908 / Χ2: 0.524 / % possible all: 68.9 |
-Processing
Software |
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Refinement | Resolution: 1.8→47.3 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 64.305 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.45 Å2 / Biso mean: 28.473 Å2 / Biso min: 10.56 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→47.3 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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