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Yorodumi- PDB-7qxk: As isolated MSOX movie series dataset 1 (0.4 MGy) of the copper n... -
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-Basic information
Entry | Database: PDB / ID: 7qxk | |||||||||
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Title | As isolated MSOX movie series dataset 1 (0.4 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) | |||||||||
Components | Copper-containing nitrite reductase | |||||||||
Keywords | OXIDOREDUCTASE / Nitrite reductase / Copper nitrite reductase / Copper-containing nitrite reductase / BrNiR / Br2DNiR / as isolated / 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 | Bradyrhizobium sp. ORS 375 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Rose, S.L. / Baba, S. / Okumura, H. / Antonyuk, S.V. / Sasaki, D. / Tosha, T. / Kumasaka, T. / Eady, R.R. / Yamamoto, M. / Hasnain, S.S. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases. Authors: Rose, S.L. / Baba, S. / Okumura, H. / Antonyuk, S.V. / Sasaki, D. / Hedison, T.M. / Shanmugam, M. / Heyes, D.J. / Scrutton, N.S. / Kumasaka, T. / Tosha, T. / Eady, R.R. / Yamamoto, M. / 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 | 7qxk.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qxk.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 7qxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/7qxk ftp://data.pdbj.org/pub/pdb/validation_reports/qx/7qxk | HTTPS FTP |
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-Related structure data
Related structure data | 7qy4C 7qycC 7zcnC 7zcoC 7zcpC 7zcqC 7zcrC 7zcsC 6zasS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 38288.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium sp. ORS 375 (bacteria) / Strain: ORS 375 / Gene: nirK, BRAO375_4030011 / Plasmid: PET-26B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0SLX7, nitrite reductase (NO-forming) | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.8 M (NH4)2SO2 and 50mM HEPES buffer pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→47.99 Å / Num. obs: 88206 / % possible obs: 98.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 11.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.015 / Rrim(I) all: 0.036 / Χ2: 0.99 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3776 / CC1/2: 0.824 / Rpim(I) all: 0.252 / Rrim(I) all: 0.418 / Χ2: 1.09 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZAS Resolution: 1.35→47.99 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.59 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.041 / 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: 15.276 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→47.99 Å
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