+Open data
-Basic information
Entry | Database: PDB / ID: 6fwf | |||||||||
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Title | Low resolution structure of Neisseria meningitidis qNOR | |||||||||
Components | Nitric-oxide reductase | |||||||||
Keywords | OXIDOREDUCTASE / reductase / membrane-bound / nitric oxide | |||||||||
Function / homology | Function and homology information nitric-oxide reductase / cytochrome bo3 ubiquinol oxidase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / aerobic respiration / respiratory electron transport chain / heme binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Neisseria meningitidis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | |||||||||
Authors | Young, D. / Antonyuk, S. / Tosha, T. / Hisano, T. / Hasnain, S. / Shiro, Y. | |||||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme. Authors: Gonska, N. / Young, D. / Yuki, R. / Okamoto, T. / Hisano, T. / Antonyuk, S. / Hasnain, S.S. / Muramoto, K. / Shiro, Y. / Tosha, T. / Adelroth, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fwf.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fwf.ent.gz | 124.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fwf_validation.pdf.gz | 871.1 KB | Display | wwPDB validaton report |
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Full document | 6fwf_full_validation.pdf.gz | 882.1 KB | Display | |
Data in XML | 6fwf_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 6fwf_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/6fwf ftp://data.pdbj.org/pub/pdb/validation_reports/fw/6fwf | HTTPS FTP |
-Related structure data
Related structure data | 3ayfS S: Starting model for refinement |
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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: 84389.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (strain alpha14) (bacteria) Strain: alpha14 / Gene: norB, NMO_1451 / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43(DE3) / References: UniProt: C6S880, nitric-oxide reductase | ||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-FE / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.48 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 400, cadmium chloride, magnesium chloride, 2-(N-morpholino)ethanesulfonic acid |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 11, 2013 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 4.2→53.64 Å / Num. obs: 11511 / % possible obs: 99.86 % / Redundancy: 14.4 % / Biso Wilson estimate: 170.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.07 / Rrim(I) all: 0.261 / Net I/σ(I): 5.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AYF Resolution: 4.2→53.64 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.82 / SU B: 137.639 / SU ML: 1.627 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.153 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: 616.17 Å2 / Biso mean: 287.437 Å2 / Biso min: 99.6 Å2
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Refinement step | Cycle: final / Resolution: 4.2→53.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.2→4.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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