+Open data
-Basic information
Entry | Database: PDB / ID: 2xxf | |||||||||
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Title | Cu metallated H254F mutant of nitrite reductase | |||||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | |||||||||
Keywords | OXIDOREDUCTASE / DENITRIFICATION | |||||||||
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 XYLOSOXIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Hough, M.A. / Eady, R.R. / 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. #1: Journal: Biochemistry / Year: 2008 Title: Identification of the Proton Channel to the Active Site Type 2 Cu Center of Nitrite Reductase: Structural and Enzymatic Properties of the His254Phe and Asn90Ser Mutants. Authors: Hough, M.A. / Eady, R.R. / 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 | 2xxf.cif.gz | 302.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xxf.ent.gz | 246.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/2xxf ftp://data.pdbj.org/pub/pdb/validation_reports/xx/2xxf | HTTPS FTP |
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-Related structure data
Related structure data | 2xwzC 2xx0C 2xx1C 1oe1S C: citing same article (ref.) 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36580.539 Da / Num. of mol.: 2 / 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) / Strain (production host): BL21 / References: UniProt: O68601 |
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-Non-polymers , 6 types, 636 molecules
#2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-MES / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDNonpolymer details | CU A1338 AND ZN A1339 WERE REFINED AT THE SAME METAL-BINDING SITE WITH OCCUPANCY SUMMING TO 1.0. ZN ...CU A1338 AND ZN A1339 WERE REFINED AT THE SAME METAL-BINDING SITE WITH OCCUPANCY SUMMING TO 1.0. ZN B1338 AND CU B1340 WERE REFINED AT THE SAME METAL-BINDING SITE WITH OCCUPANCY SUMMING TO 1.0. | |
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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: 3.02 Å3/Da / Density % sol: 56.26 % / Description: NONE |
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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: PX10.1 / Wavelength: 0.98 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2007 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→26 Å / Num. obs: 133132 / % possible obs: 97.1 % / Observed criterion σ(I): -10 / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.95 / % possible all: 78.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE1 Resolution: 1.5→95.78 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.261 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.059 / 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: 19.277 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→95.78 Å
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Refine LS restraints |
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