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Yorodumi- PDB-7zcn: Nitrite-bound MSOX movie series dataset 1 (0.8 MGy) of the copper... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zcn | |||||||||
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Title | Nitrite-bound MSOX movie series dataset 1 (0.8 MGy) of the copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) - nitrite (start) | |||||||||
Components | Copper-containing nitrite reductase | |||||||||
Keywords | OXIDOREDUCTASE / Nitrite reductase / Copper nitrite reductase / Copper-containing nitrite reductase / BrNiR / Br2DNiR / nitrite-bound / 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: 1.19 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 | 7zcn.cif.gz | 187 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zcn.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 7zcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zcn_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 7zcn_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7zcn_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 7zcn_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zcn ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zcn | HTTPS FTP |
-Related structure data
Related structure data | 7qxkC 7qy4C 7qycC 7zcoC 7zcpC 7zcqC 7zcrC 7zcsC 6zauS 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
-Protein / Sugars , 2 types, 3 molecules A
#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: Polysaccharide |
-Non-polymers , 5 types, 539 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-NO2 / #6: Chemical | #7: 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: 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: Diamond / Beamline: I24 / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 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: 1.19→75.47 Å / Num. obs: 128957 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 8.81 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.19→1.21 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 6269 / CC1/2: 0.574 / Rpim(I) all: 0.491 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZAU Resolution: 1.19→75.47 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.983 / SU B: 1.061 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / 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: 15.721 Å2
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Refinement step | Cycle: 1 / Resolution: 1.19→75.47 Å
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