+Open data
-Basic information
Entry | Database: PDB / ID: 5c4n | ||||||
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Title | CobK precorrin-6A reductase | ||||||
Components | Precorrin-6A reductase | ||||||
Keywords | OXIDOREDUCTASE / CobK precorrin-6A reductase / NADP / Rossmann fold / Precorrin | ||||||
Function / homology | precorrin-6A reductase / precorrin-6A reductase activity / Precorrin-6x reductase / Precorrin-6x reductase CbiJ/CobK / Precorrin-6x reductase domain profile. / cobalamin biosynthetic process / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Precorrin-6A reductase Function and homology information | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.63 Å | ||||||
Authors | Gu, S. / Pickersgill, R.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of CobK Authors: Gu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c4n.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c4n.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 5c4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/5c4n ftp://data.pdbj.org/pub/pdb/validation_reports/c4/5c4n | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 26076.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) (bacteria) Gene: cobK, RCAP_rcc02043 / Plasmid: pET14B / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O68098, precorrin-6A reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→42.17 Å / Num. obs: 32962 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.63→1.72 Å / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.63→42.17 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.741 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.703 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→42.17 Å
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Refine LS restraints |
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