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- PDB-6gt2: Reduced copper nitrite reductase from Achromobacter cycloclastes ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gt2 | ||||||||||||
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Title | Reduced copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography | ||||||||||||
![]() | Copper-containing nitrite reductase | ||||||||||||
![]() | OXIDOREDUCTASE / FEMTOSECOND / SF-ROX / 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. / Yamashita, K. / Gopalasingam, C.C. / Shenoy, R.T. / Hirata, K. / Ago, H. / Ueno, G. / Eady, R.R. / Antonyuk, S.V. / Yamamoto, M. / 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 | ![]() | 89.9 KB | Display | ![]() |
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PDB format | ![]() | 64.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.6 KB | Display | ![]() |
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Full document | ![]() | 444.9 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gsqC ![]() 6gt0C ![]() 6gtiC ![]() 6gtjC ![]() 6gtkC ![]() 6gtlC ![]() 6gtnC 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
#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-MLI / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.56 % |
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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 / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Oct 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.242 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→54.62 Å / Num. obs: 37489 / % possible obs: 100 % / Redundancy: 66.1 % / Biso Wilson estimate: 24.9 Å2 / R split: 0.158 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 44.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1858 / R split: 0.708 / % possible all: 100 |
Serial crystallography measurement | Pulse duration: 10 fsec. / Pulse photon energy: 437.7 keV / XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Motion control: SACLA goniometer Sample holding: Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965) Sample solvent: 3.4 M Na-malonate, pH 5.0 and 100 mM NaNO2. Support base: Mounted Hampton Cryo Loops 0.7 - 1.0 mm (HR4-965) |
Serial crystallography data reduction | Crystal hits: 581 / Frames indexed: 410 / Frames total: 581 |
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Processing
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Refinement | Resolution: 1.6→54.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.96 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.872 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→54.68 Å
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Refine LS restraints |
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