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Yorodumi- PDB-5n8f: Serial Cu nitrite reductase structures at elevated cryogenic temp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n8f | |||||||||
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Title | Serial Cu nitrite reductase structures at elevated cryogenic temperature, 240K. Dataset 1. | |||||||||
Components | Copper-containing nitrite reductase | |||||||||
Keywords | OXIDOREDUCTASE / nitrite reductase / copper enzyme / trimer / cupredoxid domain | |||||||||
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: 1.38 Å | |||||||||
Authors | Horrell, S. / Kekilli, D. / Hough, M. / Strange, R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: IUCrJ / Year: 2017 Title: Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase. Authors: Sen, K. / Horrell, S. / Kekilli, D. / Yong, C.W. / Keal, T.W. / Atakisi, H. / Moreau, D.W. / Thorne, R.E. / Hough, M.A. / Strange, R.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n8f.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n8f.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 5n8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/5n8f ftp://data.pdbj.org/pub/pdb/validation_reports/n8/5n8f | HTTPS FTP |
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-Related structure data
Related structure data | 5n8gC 5n8hC 5n8iC 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: 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-SO4 / #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: 2.02 Å3/Da / Density % sol: 39.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium citrate at pH 5.0 and 1.6 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 240 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9769 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9769 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→28.98 Å / Num. obs: 59054 / % possible obs: 97.1 % / Redundancy: 4.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.067 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3552 / Rpim(I) all: 0.529 / % possible all: 69.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BW4 Resolution: 1.38→28.98 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.159 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / 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: 12.719 Å2
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Refinement step | Cycle: 1 / Resolution: 1.38→28.98 Å
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Refine LS restraints |
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