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Yorodumi- PDB-5ofe: Cu nitrite reductase serial data at varying temperatures 190K 0.48MGy -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ofe | ||||||||||||
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Title | Cu nitrite reductase serial data at varying temperatures 190K 0.48MGy | ||||||||||||
Components | Copper-containing nitrite reductase | ||||||||||||
Keywords | OXIDOREDUCTASE / Electron transfer / nitrite reductase | ||||||||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||||||||
Authors | Horrell, S. / Kekilli, D. / Strange, R.W. / Hough, M.A. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: IUCrJ / Year: 2018 Title: Enzyme catalysis captured using multiple structures from one crystal at varying temperatures. Authors: Horrell, S. / Kekilli, D. / Sen, K. / Owen, R.L. / Dworkowski, F.S.N. / Antonyuk, S.V. / Keal, T.W. / Yong, C.W. / Eady, R.R. / Hasnain, S.S. / Strange, R.W. / Hough, M.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ofe.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ofe.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ofe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ofe_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5ofe_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5ofe_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 5ofe_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/5ofe ftp://data.pdbj.org/pub/pdb/validation_reports/of/5ofe | HTTPS FTP |
-Related structure data
Related structure data | 5of5C 5of6C 5of7C 5of8C 5ofcC 5ofdC 5offC 5ofgC 5ofhC 5og2C 5og3C 5og4C 5og5C 5og6C 5ogfC 5oggC 5i6kS 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
#1: Protein | Mass: 36621.332 Da / Num. of mol.: 1 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: Chemical | ChemComp-NO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM sodium citrate at pH 5.0 and ~1.7 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→42.5 Å / Num. obs: 25120 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rpim(I) all: 0.099 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.84→1.88 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.37 / Rpim(I) all: 0.792 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I6K Resolution: 1.84→42.5 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.89 / SU B: 3.983 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.154 / 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: 21.913 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→42.5 Å
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Refine LS restraints |
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