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Yorodumi- PDB-3x1e: Structure of copper-containing nitrite reductase from Geobacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x1e | ||||||
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Title | Structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans without chloride | ||||||
Components | Nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / beta barrel / nitrite reduction | ||||||
Function / homology | Function and homology information nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Geobacillus thermodenitrificans NG80-2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Fukuda, Y. / Inoue, T. | ||||||
Citation | Journal: To be Published Title: Structural evidence of the flexibility of the CuM site Authors: Fukuda, Y. / Inoue, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x1e.cif.gz | 157.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x1e.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 3x1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/3x1e ftp://data.pdbj.org/pub/pdb/validation_reports/x1/3x1e | HTTPS FTP |
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-Related structure data
Related structure data | 3x1fC 3x1gC 3wko C: citing same article (ref.) S: Starting model for refinement |
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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: 38427.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans NG80-2 (bacteria) Gene: nirK / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4IL26 | ||||||
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#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M acetate buffer, 5.0%(w/v) PEG 4000, 75 mM CuSO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 114829 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rsym value: 0.114 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 11494 / Rsym value: 0.37 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3WKO 3wko Resolution: 1.25→34.34 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.673 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.924 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→34.34 Å
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Refine LS restraints |
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