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- PDB-1npj: Crystal structure of H145A mutant of nitrite reductase from Alcal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1npj | ||||||
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Title | Crystal structure of H145A mutant of nitrite reductase from Alcaligenes faecalis | ||||||
![]() | Copper-containing nitrite reductase | ||||||
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Function / homology | ![]() denitrification pathway / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wijma, H.J. / Boulanger, M.J. / Molon, A. / Fittipaldi, M. / Huber, M. / Murphy, M.E. / Verbeet, M.P. / Canters, G.W. | ||||||
![]() | ![]() Title: Reconstitution of the type-1 active site of the H145G/A variants of nitrite reductase by ligand insertion Authors: Wijma, H.J. / Boulanger, M.J. / Molon, A. / Fittipaldi, M. / Huber, M. / Murphy, M.E. / Verbeet, M.P. / Canters, G.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.3 KB | Display | ![]() |
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PDB format | ![]() | 179.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1npnC ![]() 1j9qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36996.820 Da / Num. of mol.: 3 / Mutation: H145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CU / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 32.86 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: PEG 8000, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 10, 2001 / Details: osmic mirrors |
Radiation | Monochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→50 Å / Num. all: 73819 / Num. obs: 64626 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.9 Å2 |
Reflection shell | Resolution: 1.9→2.05 Å / Mean I/σ(I) obs: 4 / % possible all: 86 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 86 % / Num. unique obs: 12511 / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 4.65 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1J9Q Resolution: 1.9→31.41 Å / Data cutoff high absF: 2190210.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.8665 Å2 / ksol: 0.335529 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→31.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rwork![]() | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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