+Open data
-Basic information
Entry | Database: PDB / ID: 5c4r | ||||||
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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 / Precorrin-6A reductase Function and homology information | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.17 Å | ||||||
Authors | Gu, S. / Pickersgill, R.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Rep / Year: 2015 Title: Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap. Authors: Gu, S. / Sushko, O. / Deery, E. / Warren, M.J. / Pickersgill, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c4r.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c4r.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 5c4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/5c4r ftp://data.pdbj.org/pub/pdb/validation_reports/c4/5c4r | HTTPS FTP |
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-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: 26091.803 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(DE3) (bacteria) / References: UniProt: O68098, precorrin-6A reductase |
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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: 2.88 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8 / Details: 18% PEG3350, 0.2M NH4Cl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.13956 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.13956 Å / Relative weight: 1 |
Reflection | Resolution: 3.17→63.01 Å / Num. obs: 16610 / % possible obs: 98.16 % / Redundancy: 1.8 % / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 3.17→3.34 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.6 / % possible all: 97 |
-Processing
Software |
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Refinement | Resolution: 3.17→63.01 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 19.186 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / 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: 51.305 Å2
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Refinement step | Cycle: LAST / Resolution: 3.17→63.01 Å
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