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Yorodumi- PDB-2bo0: Crystal structure of the C130A mutant of nitrite reductase from A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bo0 | |||||||||
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Title | Crystal structure of the C130A mutant of nitrite reductase from Alcaligenes xylosoxidans | |||||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | |||||||||
Keywords | OXIDOREDUCTASE / DENITRIFICATION / NITRITE REDUCTASE / C130A / MUTANT / ELECTRON TRANSFER / COPPER / FAD / FLAVOPROTEIN / METAL- BINDING / NITRATE ASSIMILATION / PERIPLASMIC | |||||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / nitrate assimilation / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | |||||||||
Biological species | ACHROMOBACTER XYLOSOXIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Hough, M.A. / Ellis, M.J. / Antonyuk, S. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: High Resolution Structural Studies of Mutants Provide Insights Into Catalysis and Electron Transfer Processes in Copper Nitrite Reductase Authors: Hough, M.A. / Ellis, M.J. / Antonyuk, S. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bo0.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bo0.ent.gz | 177.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bo0_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 2bo0_full_validation.pdf.gz | 439.6 KB | Display | |
Data in XML | 2bo0_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 2bo0_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2bo0 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2bo0 | HTTPS FTP |
-Related structure data
Related structure data | 2bp0C 2bp8C 1ndtS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36521.430 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O68601 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 6.5 / Details: PEG 550 MME, ZNSO4, MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→100 Å / Num. obs: 74824 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.6 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NDT Resolution: 1.35→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.35→100 Å
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Refine LS restraints |
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