+Open data
-Basic information
Entry | Database: PDB / ID: 2vw6 | ||||||
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Title | NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 3 OF 3 | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / NITRITE REDUCTASE / COPPER / MICROSPECTROPHOTOMETER | ||||||
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 | Ellis, M.J. / Buffey, S.G. / Hough, M.A. / Hasnain, S.S. | ||||||
Citation | Journal: J.Synchrotron Radiat. / Year: 2008 Title: On-Line Optical and X-Ray Spectroscopies with Crystallography: An Integrated Approach for Determining Metalloprotein Structures in Functionally Well Defined States. Authors: Ellis, M.J. / Buffey, S.G. / Hough, M.A. / 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 | 2vw6.cif.gz | 156.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vw6.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vw6_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 2vw6_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 2vw6_validation.xml.gz | 33 KB | Display | |
Data in CIF | 2vw6_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vw6 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vw6 | HTTPS FTP |
-Related structure data
Related structure data | 2vw4C 2vw7C 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
#1: Protein | Mass: 36570.527 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O68601, nitrite reductase (NO-forming) #2: Chemical | ChemComp-CU / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | ZINC ION (ZN): EXOGENOUS ZINC | |
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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: 2.7 Å3/Da / Density % sol: 53.8 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 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: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.2 Å / Num. obs: 65507 / % possible obs: 97.7 % / Observed criterion σ(I): -5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE1 Resolution: 1.9→96.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.4 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→96.23 Å
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Refine LS restraints |
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