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- PDB-3x1g: H294M mutant of copper-containing nitrite reductase from Geobacil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3x1g | ||||||
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Title | H294M mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans showing two coordination geometries at the T2Cu site | ||||||
![]() | Nitrite reductase | ||||||
![]() | OXIDOREDUCTASE / beta barrel / nitrite reduction | ||||||
Function / homology | ![]() nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fukuda, Y. / Inoue, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.9 KB | Display | ![]() |
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PDB format | ![]() | 124.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
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Full document | ![]() | 453.8 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3x1eC ![]() 3x1fC ![]() 3wko C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 38420.391 Da / Num. of mol.: 1 / Mutation: H294M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: nirK / Plasmid: pET22b / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.36 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 102895 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.069 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 14968 / Rsym value: 0.573 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3WKO ![]() 3wko Resolution: 1.3→28.82 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.079 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / 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: 13.278 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→28.82 Å
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Refine LS restraints |
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