+Open data
-Basic information
Entry | Database: PDB / ID: 4fdv | ||||||
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Title | CobH from Rhodobacter capsulatus (SB1003) in complex with HBA | ||||||
Components | Precorrin-8X methylmutase | ||||||
Keywords | ISOMERASE / doubly wound sheet / sigmatrophic rearrangement / Hydrogenobyrinic acid | ||||||
Function / homology | Function and homology information precorrin-8X methylmutase / precorrin-8X methylmutase activity / cobalamin biosynthetic process Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Pickersgill, R.W. / Schroeder, S. / Deery, E. / Warren, M.J. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2012 Title: An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Authors: Deery, E. / Schroeder, S. / Lawrence, A.D. / Taylor, S.L. / Seyedarabi, A. / Waterman, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. / Pickersgill, R.W. / 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 | 4fdv.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fdv.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fdv_validation.pdf.gz | 1021 KB | Display | wwPDB validaton report |
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Full document | 4fdv_full_validation.pdf.gz | 1023.1 KB | Display | |
Data in XML | 4fdv_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 4fdv_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/4fdv ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fdv | HTTPS FTP |
-Related structure data
Related structure data | 3njrC 4au1C 1i1hS S: Starting model for refinement C: citing same article (ref.) |
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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: 22016.643 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Strain: ATCC BAA-309 / NBRC 16581 / SB1003 / Gene: cobH, RCAP_rcc02046 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: D5AV08, precorrin-8X methylmutase | ||
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#2: Chemical | ChemComp-0UK / | ||
#3: Chemical | #4: 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: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% PEG 8000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2010 / Details: Silicon 111 |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→34.7 Å / Num. all: 24994 / Num. obs: 24344 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 6.6 / Rsym value: 0.174 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I1H Resolution: 1.68→33.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.671 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.423 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→33.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.722 Å / Total num. of bins used: 20
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