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Yorodumi- PDB-5ogf: Cu nitrite reductase serial data at varying temperatures RT 0.27MGy -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ogf | ||||||||||||
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Title | Cu nitrite reductase serial data at varying temperatures RT 0.27MGy | ||||||||||||
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: 1.88 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 | 5ogf.cif.gz | 84.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ogf.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ogf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5ogf ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogf | HTTPS FTP |
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-Related structure data
Related structure data | 5of5C 5of6C 5of7C 5of8C 5ofcC 5ofdC 5ofeC 5offC 5ofgC 5ofhC 5og2C 5og3C 5og4C 5og5C 5og6C 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36522.203 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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-Non-polymers , 5 types, 133 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-NO2 / #5: Chemical | ChemComp-NO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.57 % |
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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: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.8 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→48.13 Å / Num. obs: 24354 / % possible obs: 99.5 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rpim(I) all: 0.104 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.88→1.93 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.6 / Rpim(I) all: 0.46 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I6K Resolution: 1.88→48.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.024 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.144
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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: 21.971 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→48.13 Å
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Refine LS restraints |
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