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Yorodumi- PDB-1npn: Crystal structure of a copper reconstituted H145A mutant of nitri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1npn | ||||||
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Title | Crystal structure of a copper reconstituted H145A mutant of nitrite reductase from Alcaligenes faecalis | ||||||
Components | Copper-containing nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / copper nitrite reductase | ||||||
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 | Alcaligenes faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wijma, H.J. / Boulanger, M.J. / Molon, A. / Fittipaldi, M. / Huber, M. / Murphy, M.E. / Verbeet, M.P. / Canters, G.W. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Reconstitution of the type-1 active site of the 145G/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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1npn.cif.gz | 231.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1npn.ent.gz | 181.6 KB | Display | PDB format |
PDBx/mmJSON format | 1npn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1npn ftp://data.pdbj.org/pub/pdb/validation_reports/np/1npn | HTTPS FTP |
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-Related structure data
Related structure data | 1npjC 1j9qS 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
#1: Protein | Mass: 36996.820 Da / Num. of mol.: 3 / Mutation: H145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: NIRK OR NIR / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174DE3 / References: UniProt: P38501, EC: 1.7.99.3 #2: Chemical | ChemComp-CU / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.12 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 86849 / Num. obs: 78136 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.5 Å2 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 0.041 / Mean I/σ(I) obs: 7 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J9Q Resolution: 1.8→33.28 Å / Data cutoff high absF: 2292803.12 / 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: 55.7396 Å2 / ksol: 0.345549 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.1 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→33.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Total num. of bins used: 6
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Xplor file |
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