+Open data
-Basic information
Entry | Database: PDB / ID: 1j9s | ||||||
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Title | Crystal structure of nitrite soaked oxidized H255N AFNIR | ||||||
Components | COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / cupredoxin fold copper nitrite | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Boulanger, M.J. / Murphy, M.E. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate Authors: Boulanger, M.J. / Murphy, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j9s.cif.gz | 223.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j9s.ent.gz | 176.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/1j9s ftp://data.pdbj.org/pub/pdb/validation_reports/j9/1j9s | 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: 36854.605 Da / Num. of mol.: 3 / Fragment: RESIDUES 40-376 / Mutation: H255N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 DE3 / 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: 2.1 Å3/Da / Density % sol: 41.45 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 6000, sodium acetate, copper chloride, sodium nitrite, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 10, 2000 / Details: osmic mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 74119 / Num. obs: 66707 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 5.35 / % possible all: 70.1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % possible obs: 90 % / Redundancy: 7.71 % |
Reflection shell | *PLUS % possible obs: 70.1 % / Num. unique obs: 8527 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2734562.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.95 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.226 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.184 |