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Yorodumi- PDB-2dj5: Crystal Structure of the vitamin B12 biosynthetic cobaltochelatas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dj5 | ||||||
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Title | Crystal Structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus | ||||||
Components | Sirohydrochlorin cobaltochelatase | ||||||
Keywords | LYASE / beta-alpha-beta / parallel beta sheet | ||||||
Function / homology | Function and homology information sirohydrochlorin cobaltochelatase / anaerobic cobalamin biosynthetic process / sirohydrochlorin cobaltochelatase activity / tetrapyrrole binding / cobalt ion binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Yin, J. / Cherney, M.M. / James, M.N.G. | ||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2006 Title: Crystal Structure of the Vitamin B(12) Biosynthetic Cobaltochelatase, CbiX (S), from Archaeoglobus Fulgidus Authors: Yin, J. / Xu, L.X. / Cherney, M.M. / Raux-Deery, E. / Bindley, A.A. / Savchenko, A. / Walker, J.R. / Cuff, M.E. / Warren, M.J. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dj5.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dj5.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/2dj5 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/2dj5 | HTTPS FTP |
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-Related structure data
Related structure data | 1tjnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15190.501 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: cbiX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) STAR References: UniProt: O29537, sirohydrochlorin cobaltochelatase #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: 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: 2.81 Å3/Da / Density % sol: 56.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 1.9M ammonium phosphate pH6.8, 4% 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.019943 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2004 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.019943 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→60 Å / Num. all: 12517 / Num. obs: 8637 / % possible obs: 69 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.9 / % possible all: 48.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TJN Resolution: 2.55→54.3 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.55→54.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.62 Å
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