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Yorodumi- PDB-2xwz: STRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xwz | ||||||
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Title | STRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / PROTON CHANNEL / DENITRIFICATION. | ||||||
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: 2.34 Å | ||||||
Authors | Antonyuk, S.V. / Leferink, N.G.H. / Han, C. / Heyes, D.J. / Rigby, S.E.J. / Hough, M.A. / Eady, R.R. / Scrutton, N.S. / Hasnain, S.S. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase. Authors: Leferink, N.G.H. / Han, C. / Antonyuk, S.V. / Heyes, D.J. / Rigby, S.E.J. / Hough, M.A. / Eady, R.R. / Scrutton, N.S. / Hasnain, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xwz.cif.gz | 431.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xwz.ent.gz | 353.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xwz_validation.pdf.gz | 530.4 KB | Display | wwPDB validaton report |
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Full document | 2xwz_full_validation.pdf.gz | 543 KB | Display | |
Data in XML | 2xwz_validation.xml.gz | 88.4 KB | Display | |
Data in CIF | 2xwz_validation.cif.gz | 127.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/2xwz ftp://data.pdbj.org/pub/pdb/validation_reports/xw/2xwz | HTTPS FTP |
-Related structure data
Related structure data | 2xx0C 2xx1C 2xxfC 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
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 36571.512 Da / Num. of mol.: 6 / Fragment: RESIDUES 26-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Strain: IW2 IWASAKI / Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O68601, nitrite reductase (NO-forming) |
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-Non-polymers , 6 types, 1644 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-NO2 / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-ACT / #6: Chemical | #7: 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: 6.37 Å3/Da / Density % sol: 80 % / Description: NONE |
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Crystal grow | pH: 4.25 Details: 1.8 M LITHIUM SULFATE, 100MM ACETATE BUFFER PH 4.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→43.97 Å / Num. obs: 232880 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.34→2.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE1 Resolution: 2.34→43.97 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.629 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.832 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→43.97 Å
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