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Yorodumi- PDB-1qgo: ANAEROBIC COBALT CHELATASE IN COBALAMIN BIOSYNTHESIS FROM SALMONE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qgo | ||||||
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Title | ANAEROBIC COBALT CHELATASE IN COBALAMIN BIOSYNTHESIS FROM SALMONELLA TYPHIMURIUM | ||||||
Components | ANAEROBIC COBALAMIN BIOSYNTHETIC COBALT CHELATASE | ||||||
Keywords | METAL BINDING PROTEIN / COBALAMIN / VITAMIN B12 / METAL ION CHELATION / CHELATASE / COBALT PRECORRIN / CBIK | ||||||
Function / homology | Function and homology information sirohydrochlorin cobaltochelatase / anaerobic cobalamin biosynthetic process / sirohydrochlorin cobaltochelatase activity / tetrapyrrole binding / porphyrin-containing compound biosynthetic process / cobalt ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.4 Å | ||||||
Authors | Schubert, H.L. / Raux, E. / Warren, M.J. / Wilson, K.S. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Common chelatase design in the branched tetrapyrrole pathways of heme and anaerobic cobalamin synthesis. Authors: Schubert, H.L. / Raux, E. / Wilson, K.S. / Warren, M.J. #1: Journal: J.Bacteriol. / Year: 1997 Title: A Role for Salmonella Typhimurium Cbik in Cobalamin (Vitamin B12) and Siroheme Biosynthesis Authors: Raux, E. / Thermes, C. / Heathcote, P. / Rambauch, A. / Warren, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qgo.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qgo.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/1qgo ftp://data.pdbj.org/pub/pdb/validation_reports/qg/1qgo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29273.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Description: HIS-TAGGED RECOMBINANT GENE / Gene: CBIK / Plasmid: PAR8668 / Gene (production host): CBIK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): LYSS / References: UniProt: Q05592 | ||
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#2: Chemical | #3: 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: 3.35 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 10-15% PEG (MW 4000), 0.2 M LI2SO4, 0.1 M TRIS PH 8.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998 / Details: MIRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 16699 / % possible obs: 99.5 % / Redundancy: 15 % / Biso Wilson estimate: 36.21 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4 / % possible all: 99.8 |
Reflection | *PLUS Num. all: 16699 / Num. obs: 16597 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.1956 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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