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Yorodumi- PDB-2fjs: Crystal Structure of Anaerobically Reduced Wild Type Nitrite Redu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fjs | ||||||
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Title | Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase from A. faecalis | ||||||
Components | Copper-containing nitrite reductase | ||||||
Keywords | OXIDOREDUCTASE / blue copper protein / cupredoxin fold | ||||||
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: 1.85 Å | ||||||
Authors | Tocheva, E.I. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Effect of the methionine ligand on the reorganization energy of the type-1 copper site of nitrite reductase. Authors: Wijma, H.J. / MacPherson, I. / Farver, O. / Tocheva, E.I. / Pecht, I. / Verbeet, M.P. / Murphy, M.E.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 | 2fjs.cif.gz | 228.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fjs.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 2fjs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fjs_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
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Full document | 2fjs_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 2fjs_validation.xml.gz | 47.4 KB | Display | |
Data in CIF | 2fjs_validation.cif.gz | 72.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/2fjs ftp://data.pdbj.org/pub/pdb/validation_reports/fj/2fjs | HTTPS FTP |
-Related structure data
Related structure data | 2b08C 1snrS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 36422.133 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Gene: nirK, nir / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P38501, nitrite reductase (NO-forming) |
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-Non-polymers , 5 types, 1123 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-TRS / | #6: 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: 41.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 8-10% PEG 4000, 0.1 M NaOAC, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2005 / 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: 1.85→30 Å / Num. obs: 72738 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.116 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1SNR Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.373 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 1.85 / ESU R: 0.15 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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