+Open data
-Basic information
Entry | Database: PDB / ID: 3cb0 | ||||||
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Title | CobR | ||||||
Components | 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / Corrin reductase / CobR / six-stranded anti-parallel beta-barrel | ||||||
Function / homology | Function and homology information 4-hydroxyphenylacetate 3-monooxygenase / 4-hydroxyphenylacetate 3-monooxygenase activity / oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / FMN binding Similarity search - Function | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Lawrence, A.D. / Warren, M.J. / Pickersgill, R.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Identification, characterization, and structure/function analysis of a corrin reductase involved in adenosylcobalamin biosynthesis Authors: Lawrence, A.D. / Deery, E. / McLean, K.J. / Munro, A.W. / Pickersgill, R.W. / Rigby, S.E. / 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 | 3cb0.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cb0.ent.gz | 127.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cb0_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3cb0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3cb0_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 3cb0_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/3cb0 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/3cb0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 18747.221 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: cobR / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YHT7, EC: 1.14.13.3 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 49.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.5-1.0M Li2S04, 15-20% polyethylene glycol 800, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.8 Å / Num. obs: 97683 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 6.8 / Num. unique all: 14080 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→42.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.56 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.097 / 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: 16.008 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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