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- PDB-6zar: As-isolated copper nitrite reductase from Bradyrhizobium sp. ORS ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zar | ||||||
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Title | As-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.1 A resolution (unrestrained, full matrix refinement by SHELX) | ||||||
![]() | Copper-containing nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing nitrite reductase / BrNiR / Br2dNiR / as-isolated / atomic resolution | ||||||
Function / homology | ![]() denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.7 KB | Display | ![]() |
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PDB format | ![]() | 145.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zasC ![]() 6zatC ![]() 6zauC ![]() 6zavC ![]() 6zawC ![]() 6zaxC ![]() 6thfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 38086.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ORS 375 / Gene: nirK, BRAO375_4030011 / Plasmid: pET-26b(+) / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 654 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.8 M Ammonium sulphate, 50mM Hepes buff |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2019 / Details: mirrors |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97634 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→47.72 Å / Num. obs: 162755 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 7.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.038 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7743 / CC1/2: 0.63 / Rpim(I) all: 0.499 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6THF Resolution: 1.1→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.02 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4 %
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.2 Å2 | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 179 / Occupancy sum hydrogen: 2541 / Occupancy sum non hydrogen: 3230 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→30 Å
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Refine LS restraints | Type: s_approx_iso_adps | |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.1→1.29 Å
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