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Yorodumi- PDB-2cbf: THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cbf | ||||||
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Title | THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF, FROM BACILLUS MEGATERIUM, WITH THE HIS-TAG CLEAVED OFF | ||||||
Components | COBALT-PRECORRIN-4 TRANSMETHYLASE | ||||||
Keywords | METHYLTRANSFERASE / PRECORRIN-4 METHYLTRANSFERASE / METHYLASE / COBALAMIN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information cobalt-precorrin-4 methyltransferase / precorrin-4 C11-methyltransferase activity / cobalamin biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Schubert, H.L. / Raux, E. / Woodcock, S.C. / Warren, M.J. / Wilson, K.S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase. Authors: Schubert, H.L. / Wilson, K.S. / Raux, E. / Woodcock, S.C. / Warren, M.J. #1: Journal: Eur.J.Biochem. / Year: 1998 Title: Cobalamin (Vitamin B12) Biosynthesis--Cloning, Expression and Crystallisation of the Bacillus Megaterium S-Adenosyl-L-Methionine-Dependent Cobalt-Precorrin-4 Transmethylase Cbif Authors: Raux, E. / Schubert, H.L. / Woodcock, S.C. / Wilson, K.S. / 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 | 2cbf.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cbf.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 2cbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cbf_validation.pdf.gz | 806.1 KB | Display | wwPDB validaton report |
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Full document | 2cbf_full_validation.pdf.gz | 903.8 KB | Display | |
Data in XML | 2cbf_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 2cbf_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/2cbf ftp://data.pdbj.org/pub/pdb/validation_reports/cb/2cbf | HTTPS FTP |
-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: 25504.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Cell line: BL21 / Gene: CBIF / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS References: UniProt: O87696, precorrin-4 C11-methyltransferase |
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#2: Chemical | ChemComp-SAH / |
Compound details | THE ROTATION MATRIX TO SUPERIMPOSE THIS STRUCTURE TO THE PO4-BOUND STRUCTURE AT 2.1 ANGSTROM ...THE ROTATION MATRIX TO SUPERIMPOS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 64 % | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: MSC MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 5524 / % possible obs: 95 % / Rsym value: 0.082 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3.1→3.21 Å / Rsym value: 0.472 / % possible all: 94 |
Reflection | *PLUS % possible obs: 95.3 % / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 93.7 % / Rmerge(I) obs: 0.489 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CBIF-FULL LENGTH CRYSTALLIZED IN PO4 Resolution: 3.1→20 Å
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 / Rfactor Rfree: 0.283 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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