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Yorodumi- PDB-1kcb: Crystal Structure of a NO-forming Nitrite Reductase Mutant: an An... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kcb | ||||||
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Title | Crystal Structure of a NO-forming Nitrite Reductase Mutant: an Analog of a Transition State in Enzymatic Reaction | ||||||
Components | Nitrite Reductase | ||||||
Keywords | OXIDOREDUCTASE / copper-containing nitrite reductase / BETA BARREL | ||||||
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 | Achromobacter cycloclastes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å | ||||||
Authors | Liu, S.Q. / Chang, T. / Liu, M.Y. / LeGall, J. / Chang, W.C. / Zhang, J.P. / Liang, D.C. / Chang, W.R. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2003 Title: Crystal structure of a NO-forming nitrite reductase mutant: an analog of a transition state in enzymatic reaction Authors: Liu, S.Q. / Chang, T. / Liu, M.Y. / LeGall, J. / Chang, W.C. / Zhang, J.P. / Liang, D.C. / Chang, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kcb.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kcb.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 1kcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kcb ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kcb | HTTPS FTP |
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-Related structure data
Related structure data | 1nieS 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 on special symmetry positions |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: y, z, x and z, x, y |
-Components
#1: Protein | Mass: 37075.766 Da / Num. of mol.: 1 / Mutation: I257E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Achromobacter cycloclastes (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P25006, EC: 1.7.99.3 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: ammonium sulfate, Potassium Phosphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→10 Å / Num. all: 37951 / Num. obs: 37951 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 48.2 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.65 Å / Num. obs: 37954 / % possible obs: 99.9 % / Num. measured all: 393521 |
Reflection shell | *PLUS Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1NIE Resolution: 1.65→9.97 Å / σ(F): 4 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 1.65→9.97 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rwork: 0.17 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |