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Yorodumi- PDB-6gtj: Neutron crystal structure for copper nitrite reductase from Achro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gtj | ||||||||||||
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Title | Neutron crystal structure for copper nitrite reductase from Achromobacter Cycloclastes at 1.8 A resolution | ||||||||||||
Components | Copper-containing nitrite reductase | ||||||||||||
Keywords | OXIDOREDUCTASE / Perdueteration / NITRITE REDUCTASE / electron transfer | ||||||||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | ||||||||||||
Biological species | Achromobacter cycloclastes (bacteria) | ||||||||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | ||||||||||||
Authors | Antonyuk, S.V. / Blakeley, M.P. / Halsted, T.P. / Eady, R.R. / Hasnain, S.S. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Iucrj / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gtj.cif.gz | 143.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gtj.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gtj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gtj_validation.pdf.gz | 333.4 KB | Display | wwPDB validaton report |
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Full document | 6gtj_full_validation.pdf.gz | 333.9 KB | Display | |
Data in XML | 6gtj_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 6gtj_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/6gtj ftp://data.pdbj.org/pub/pdb/validation_reports/gt/6gtj | HTTPS FTP |
-Related structure data
Related structure data | 6gsqC 6gt0C 6gt2C 6gtiC 6gtkC 6gtlC 6gtnC 2bw4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 37059.809 Da / Num. of mol.: 1 / Fragment: UNP residues 39-378 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Gene: nirK / Production host: Escherichia coli (E. coli) / References: UniProt: P25006, nitrite reductase (NO-forming) | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 35 % / Description: pyramidal shape |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.2M Ammonium sulphate, Citrate buffer pH 5 all deuterium based |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: NUCLEAR REACTOR / Site: ILL / Beamline: LADI III / Wavelength: 3.05 - 4.00 | |||||||||
Detector | Type: LADI III / Detector: DIFFRACTOMETER / Date: Jul 24, 2015 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→40 Å / Num. obs: 24728 / % possible obs: 85.5 % / Redundancy: 6.5 % / Rpim(I) all: 0.063 / Net I/σ(I): 7.9 | |||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1858 / Rpim(I) all: 0.13 / % possible all: 69.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BW4 Resolution: 1.801→32.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 26.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.8825 Å
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