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Yorodumi- PDB-2bp8: M144Q Structure of nitrite reductase from Alcaligenes xylosoxidans -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bp8 | ||||||
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Title | M144Q Structure of nitrite reductase from Alcaligenes xylosoxidans | ||||||
Components | (DISSIMILATORY COPPER-CONTAINING NITRITE ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / DENTRIFICATION / NITRITE REDUCTASE / M168Q / MUTANT / ELECTRON TRANSFER / 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: 1.9 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 | 2bp8.cif.gz | 162.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bp8.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bp8_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 2bp8_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 2bp8_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 2bp8_validation.cif.gz | 52.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bp8 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bp8 | HTTPS FTP |
-Related structure data
Related structure data | 2bo0C 2bp0C 1oe1S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-DISSIMILATORY COPPER-CONTAINING NITRITE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36568.445 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: Protein | Mass: 36568.445 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 |
-Non-polymers , 4 types, 810 molecules
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYTIC ACTIVITY ENGINEERED |
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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: 2.74 Å3/Da / Density % sol: 54.72 % |
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-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: 1.9→28 Å / Num. obs: 57774 / % possible obs: 86.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE1 Resolution: 1.9→28 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.775 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→28 Å
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Refine LS restraints |
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