[English] 日本語
Yorodumi- PDB-8rfw: High pH (8.0) as-isolated MSOX movie series dataset 2 of the copp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rfw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | High pH (8.0) as-isolated MSOX movie series dataset 2 of the copper nitrite reductase from Bradyrhizobium sp. ORS375 (two-domain) [0.82 MGy] | |||||||||
Components | Copper-containing nitrite reductase | |||||||||
Keywords | OXIDOREDUCTASE / Copper nitrite reductase / Copper-containing nitrite reductase / Br2DNiR / high pH / as-isolated / resting state / 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: 1.33 Å | |||||||||
Authors | Rose, S.L. / Ferroni, F.M. / Antonyuk, S.V. / Eady, R.R. / Hasnain, S.S. | |||||||||
Funding support | United Kingdom, Argentina, 2items
| |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2024 Title: Spectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases. Authors: Rose, S.L. / Ferroni, F.M. / Horrell, S. / Brondino, C.D. / Eady, R.R. / Jaho, S. / Hough, M.A. / Owen, R.L. / Antonyuk, S.V. / Hasnain, S.S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8rfw.cif.gz | 178 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8rfw.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 8rfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/8rfw ftp://data.pdbj.org/pub/pdb/validation_reports/rf/8rfw | HTTPS FTP |
---|
-Related structure data
Related structure data | 8r8sC 8rflC 8rfoC 8rfpC 8rfqC 8rfrC 8rfsC 8rftC 8rfuC 8rfvC 8rfxC 8rfyC 8rg8C 8rg9C 8rgbC 8rgcC 8rgdC 8ru9C 8rurC 8ryjC 8ryrC 8ryuC 8ryvC 8s0wC 8s2qC 8s5xC 8s5yC 8s63C 8s64C 8s68C 8s69C 9evmC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 38144.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium sp. ORS 375 (bacteria) / Gene: nirK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0SLX7 |
---|---|
#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose |
-Non-polymers , 4 types, 454 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.05 M HEPES pH 5.5, 1.8 M Ammonium Sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.775 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.775 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→37.87 Å / Num. obs: 93708 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 13.37 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.043 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4615 / CC1/2: 0.364 / Rpim(I) all: 0.736 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→35 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.046 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.739 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.33→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|