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- PDB-6zat: Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. OR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zat | ||||||
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Title | Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.0 A resolution (unrestrained full matrix refinement by SHELX) | ||||||
![]() | Copper-containing nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing / BrNiR / Br2dNiR / nitrite-bound / substrate-bound / 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 | ![]() | 194.6 KB | Display | ![]() |
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PDB format | ![]() | 150.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 39.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zarC ![]() 6zasC ![]() 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 , 6 types, 720 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-SO4 / #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 54.13 % / Description: blue big cubes |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.6/1.8 M (NH4)2SO4 and 50mM HEPES buffer pH 5/ pH 5.5 PH range: 5.5 |
-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: 0.86999 Å / Relative weight: 1 |
Reflection | Resolution: 1→53.39 Å / Num. obs: 216881 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 6.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Net I/av σ(I): 10.8 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 10633 / CC1/2: 0.388 / Rpim(I) all: 0.731 / % possible all: 94.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6THF Resolution: 1→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.015 / 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: 16 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 139 / Occupancy sum hydrogen: 2485 / Occupancy sum non hydrogen: 3350.3 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.026 Å
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