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Yorodumi- PDB-6zud: Cu nitrite reductase from Achromobacter cycloclastes: MSOX series... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zud | ||||||||||||
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Title | Cu nitrite reductase from Achromobacter cycloclastes: MSOX series at 170K, dose point 3 | ||||||||||||
Components | Copper-containing nitrite reductase | ||||||||||||
Keywords | OXIDOREDUCTASE / Cu nitrite reductase / nitrosyl / copper / MSOX | ||||||||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | ||||||||||||
Biological species | Achromobacter cycloclastes (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||||||||
Authors | Hough, M.A. / Antonyuk, S.V. / Strange, R.W. / Hasnain, S.S. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Chem Sci / Year: 2020 Title: Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis. Authors: Hough, M.A. / Conradie, J. / Strange, R.W. / Antonyuk, S.V. / Eady, R.R. / Ghosh, A. / Hasnain, S.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zud.cif.gz | 178.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zud.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 6zud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/6zud ftp://data.pdbj.org/pub/pdb/validation_reports/zu/6zud | HTTPS FTP |
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-Related structure data
Related structure data | 6zu6C 6zuaC 6zubC 6zutC 2bw4S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36621.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: nirK / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming) |
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-Non-polymers , 5 types, 584 molecules
#2: Chemical | #3: Chemical | ChemComp-NO2 / | #4: Chemical | #5: Chemical | ChemComp-MLI / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 1.97 Å3/Da / Density % sol: 37.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.75 Details: 1.6M AMMONIUM SULPHATE, 100MM REMARK 280 SODIUM ACETATE, PH 4.75 |
-Data collection
Diffraction | Mean temperature: 170 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→42.6 Å / Num. obs: 115774 / % possible obs: 99.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 7.4 Å2 / Rpim(I) all: 0.037 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 16660 / Rpim(I) all: 0.332 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bw4 Resolution: 1.1→38.96 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 78.23 Å2 / Biso mean: 12.811 Å2 / Biso min: 5.84 Å2
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Refinement step | Cycle: final / Resolution: 1.1→38.96 Å
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LS refinement shell | Resolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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