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Yorodumi- PDB-5i6p: Crystal Structure of Copper Nitrite Reductase at 100K after 27.60 MGy -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i6p | ||||||
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Title | Crystal Structure of Copper Nitrite Reductase at 100K after 27.60 MGy | ||||||
Components | Copper-containing nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / Copper Nitrite Reductase / Reaction Mechanism / Serial Crystallography | ||||||
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: 1.56 Å | ||||||
Authors | Horrell, S. / Hough, M.A. / Strange, R.W. | ||||||
Citation | Journal: Iucrj / Year: 2016 Title: Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal. Authors: Horrell, S. / Antonyuk, S.V. / Eady, R.R. / Hasnain, S.S. / 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 | 5i6p.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i6p.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 5i6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/5i6p ftp://data.pdbj.org/pub/pdb/validation_reports/i6/5i6p | HTTPS FTP |
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-Related 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: 36391.008 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 BL21(DE3) (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming) | ||||
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#2: Chemical | #3: Chemical | ChemComp-NO2 / | #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: 1.99 Å3/Da / Density % sol: 38.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.7 M Ammonium Sulphate, 0.1 M Sodium Acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2013 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.56→42.62 Å / Num. obs: 39170 / % possible obs: 95.7 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.026 / Rrim(I) all: 0.057 / Net I/σ(I): 14.3 / Num. measured all: 164926 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→42.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.702 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 73.96 Å2 / Biso mean: 27.197 Å2 / Biso min: 15.5 Å2
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Refinement step | Cycle: final / Resolution: 1.56→42.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 Å / Total num. of bins used: 20
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