+Open data
-Basic information
Entry | Database: PDB / ID: 3bnh | ||||||
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Title | W. succinogenes NrfA Y218F Nitrite Complex | ||||||
Components | Cytochrome c-552 | ||||||
Keywords | OXIDOREDUCTASE / c-type cytochrome / nitrite reductase / nitrite complex / Calcium / Electron transport / Heme / Iron / Metal-binding / Periplasm / Transport | ||||||
Function / homology | Function and homology information nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / : / nitrate assimilation / outer membrane-bounded periplasmic space / calcium ion binding / heme binding Similarity search - Function | ||||||
Biological species | Wolinella succinogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Lukat, P. / Einsle, O. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Binding and Reduction of Sulfite by Cytochrome c Nitrite Reductase Authors: Lukat, P. / Rudolf, M. / Stach, P. / Messerschmidt, A. / Kroneck, P.M.H. / Simon, J. / Einsle, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bnh.cif.gz | 135.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bnh.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/3bnh ftp://data.pdbj.org/pub/pdb/validation_reports/bn/3bnh | HTTPS FTP |
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-Related structure data
Related structure data | 3bnfC 3bngC 3bnjC 1fs7S S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55327.605 Da / Num. of mol.: 1 / Mutation: Y218F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: nrfA Y218F / Production host: Wolinella succinogenes (bacteria) References: UniProt: Q9S1E5, nitrite reductase (cytochrome; ammonia-forming) |
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-Non-polymers , 7 types, 659 molecules
#2: Chemical | ChemComp-NO2 / | ||||||||
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#3: Chemical | ChemComp-CA / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | #7: Chemical | ChemComp-HEM / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: PEG 4000, ammonium sulfate, yttrium chloride, acetate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 22, 2007 |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 69720 / Num. obs: 69581 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rsym value: 0.11 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.75→1.85 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.687 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FS7 Resolution: 1.75→29.49 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.412 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.101 / ESU R Free: 0.103 / 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: 29.209 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→29.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.747→1.792 Å / Total num. of bins used: 20
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