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Yorodumi- PDB-6zax: Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. OR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zax | ||||||
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Title | Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at low dose (0.5 MGy) | ||||||
Components | Copper-containing nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing nitrite reductase / BrNiR / Br2dNiR / substrate-bound / nitrite-bound / low dose / synchrotron | ||||||
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. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Rose, S.L. / Antonyuk, S.V. / Sasaki, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Ago, H. / Eady, R.R. / Tosha, T. / Yamamoto, M. / Hasnain, S.S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Adv / Year: 2021 Title: An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. Authors: Rose, S.L. / Antonyuk, S.V. / Sasaki, D. / Yamashita, K. / Hirata, K. / Ueno, G. / Ago, H. / Eady, R.R. / Tosha, T. / 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 | 6zax.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zax.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 6zax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/6zax ftp://data.pdbj.org/pub/pdb/validation_reports/za/6zax | HTTPS FTP |
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-Related structure data
Related structure data | 6zarC 6zasC 6zatC 6zauC 6zavC 6zawC 6thfS 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 / Sugars , 2 types, 4 molecules A
#1: Protein | Mass: 38086.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium sp. (strain ORS 375) (bacteria) Strain: ORS 375 / Gene: nirK, BRAO375_4030011 / Plasmid: Pet26b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0SLX7, nitrite reductase (NO-forming) |
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#2: Polysaccharide |
-Non-polymers , 5 types, 507 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-NO2 / | #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: 2.72 Å3/Da / Density % sol: 54.83 % / Description: blue cubes |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.6 M (NH4)2SO4 and 50mM HEPES buffer pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→48.15 Å / Num. obs: 65671 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.48→1.5 Å / Rmerge(I) obs: 1.638 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4753 / CC1/2: 0.541 / Rpim(I) all: 0.667 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6THF Resolution: 1.48→48.15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.315 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.062 / 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: 96.41 Å2 / Biso mean: 21.131 Å2 / Biso min: 6.48 Å2
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Refinement step | Cycle: final / Resolution: 1.48→48.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.517 Å / Rfactor Rfree error: 0
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