+Open data
-Basic information
Entry | Database: PDB / ID: 6hiu | ||||||
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Title | Cytochrome P460 from Methylococcus capsulatus (Bath) | ||||||
Components | Cytochrome P460 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome / NO / CO / methanotroph | ||||||
Function / homology | Cytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / HEME C / Cytochrome P460 Function and homology information | ||||||
Biological species | Methylococcus capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å | ||||||
Authors | Adams, H. / Chicano, T.M. / Hough, M.A. | ||||||
Citation | Journal: Chem Sci / Year: 2019 Title: One fold, two functions: cytochrome P460 and cytochromec'-beta from the methanotrophMethylococcus capsulatus(Bath). Authors: Adams, H.R. / Krewson, C. / Vardanega, J.E. / Fujii, S. / Moreno, T. / Sambongi, Y. / Svistunenko, D. / Paps, J. / Andrew, C.R. / Hough, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hiu.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hiu.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hiu_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6hiu_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6hiu_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6hiu_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/6hiu ftp://data.pdbj.org/pub/pdb/validation_reports/hi/6hiu | 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: 17366.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria) Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: MCA0524 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1UBD9 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8 Details: 2microlitres of 15mg/ml protein in 20mM Tris buffer, pH8, with an equivalent volume of reservoir solution containing 0.1M Tris, 2.4M Ammonium sulfate pH8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.928 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→46.62 Å / Num. obs: 70585 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.02 / Rrim(I) all: 0.048 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.36→1.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3431 / CC1/2: 0.486 / Rpim(I) all: 0.562 / Rrim(I) all: 1.195 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.36→42.67 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.84 Å2 / Biso mean: 19.701 Å2 / Biso min: 9.78 Å2
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Refinement step | Cycle: final / Resolution: 1.36→42.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.36→1.395 Å / Total num. of bins used: 20
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