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Open data
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Basic information
Entry | Database: PDB / ID: 6gti | ||||||||||||
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Title | Achromobacter cycloclastes copper nitrite reductase at pH 5.0 | ||||||||||||
![]() | Copper-containing nitrite reductase | ||||||||||||
![]() | OXIDOREDUCTASE / NITRITE REDUCTASE | ||||||||||||
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 | ![]() | ||||||||||||
![]() | Halsted, T.P. / Eady, R.R. / Antonyuk, S.V. / Hasnain, S.S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. Authors: Halsted, T.P. / Yamashita, K. / Gopalasingam, C.C. / Shenoy, R.T. / Hirata, K. / Ago, H. / Ueno, G. / Blakeley, M.P. / Eady, R.R. / Antonyuk, S.V. / 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 | ![]() | 95.6 KB | Display | ![]() |
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PDB format | ![]() | 69 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
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Full document | ![]() | 452.7 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gsqC ![]() 6gt0C ![]() 6gt2C ![]() 6gtjC ![]() 6gtkC ![]() 6gtlC ![]() 6gtnC ![]() 2bw4S C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 40819.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NO2 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.17 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.2 M ammonium sulphate, 100 mM citrate buffer, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→7.9 Å / Num. obs: 46390 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.036 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2247 / CC1/2: 0.653 / Rpim(I) all: 0.473 / % possible all: 98.3 |
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Processing
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Refinement | Starting model: 2BW4 Resolution: 1.5→7.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.333 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.42 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→7.9 Å
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Refine LS restraints |
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