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- PDB-6zau: Damage-free nitrite-bound copper nitrite reductase from Bradyrhiz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zau | ||||||
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Title | Damage-free nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | ||||||
![]() | Copper-containing nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / nitrite reductase / copper nitrite reductase / copper-containing nitrite reductase / BrNiR / Br2dNiR / substrate-bound / nitrite-bound / damage-free / XFEL | ||||||
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 | ![]() | 183.3 KB | Display | ![]() |
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PDB format | ![]() | 145.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zarC ![]() 6zasC ![]() 6zatC ![]() 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 / Sugars , 2 types, 3 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 / Production host: ![]() ![]() |
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#2: Polysaccharide |
-Non-polymers , 6 types, 449 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | #7: Chemical | ChemComp-NO2 / | #8: 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: 56 % / Description: blue cubes |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.6/1.8 M (NH4)2SO4 and 50mM HEPES buffer pH 5/ pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→75.63 Å / Num. obs: 99872 / % possible obs: 99.9 % / Redundancy: 73.4 % / Biso Wilson estimate: 16.3 Å2 / CC1/2: 0.951 / R split: 0.163 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 1.3→1.35 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 12315 / CC1/2: 0.016 / R split: 1.126 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6THF Resolution: 1.3→29.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.864 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.052 / 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: 63.76 Å2 / Biso mean: 22.613 Å2 / Biso min: 10.03 Å2
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Refinement step | Cycle: final / Resolution: 1.3→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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