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Yorodumi- PDB-2jfc: M144L mutant of Nitrite Reductase from Alcaligenes xylosoxidans i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jfc | ||||||
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Title | M144L mutant of Nitrite Reductase from Alcaligenes xylosoxidans in space group P212121 | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSFER. NITRITE REDUCTASE / DENITRIFICATION / COMPLEX FORMATION / MUTANT / COPPER / METAL-BINDING / ALCALIGENES XYLOSOXIDANS | ||||||
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: 2.4 Å | ||||||
Authors | Paraskevopoulos, K. / Hough, M.A. / Sawers, R.G. / Eady, R.R. / Hasnain, S.S. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2007 Title: The Structure of the met144Leu Mutant of Copper Nitrite Reductase from Alcaligenes Xylosoxidans Provides the First Glimpse of a Protein-Protein Complex with Azurin II. Authors: Paraskevopoulos, K. / Hough, M.A. / Sawers, R.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 | 2jfc.cif.gz | 404.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jfc.ent.gz | 329.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jfc_validation.pdf.gz | 397.2 KB | Display | wwPDB validaton report |
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Full document | 2jfc_full_validation.pdf.gz | 408.1 KB | Display | |
Data in XML | 2jfc_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 2jfc_validation.cif.gz | 62.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/2jfc ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jfc | HTTPS FTP |
-Related structure data
Related structure data | 2bo0S S: Starting model for refinement |
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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
#1: Protein | Mass: 36424.359 Da / Num. of mol.: 6 / Fragment: RESIDUES 26-360 / 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, nitrite reductase (NO-forming) #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, MET 168 TO LEU ENGINEERED RESIDUE IN CHAIN B, MET 168 TO LEU ...ENGINEERED | Sequence details | M144L MUTATION | |
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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: 5.89 Å3/Da / Density % sol: 79.8 % |
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Crystal grow | pH: 4.2 / Details: pH 4.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.8 Å / Num. obs: 213297 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / % possible all: 71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BO0 Resolution: 2.4→49.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.553 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.137 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→49.7 Å
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