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Yorodumi- PDB-2vm4: Structure of Alcaligenes xylosoxidans nitrite reductase in space ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vm4 | ||||||
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Title | Structure of Alcaligenes xylosoxidans nitrite reductase in space group R3 - 2 of 2 | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / DENITRIFICATION / NITRITE REDUCTASE / ORDERED MECHANISM | ||||||
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: 1.9 Å | ||||||
Authors | Hough, M.A. / Antonyuk, S.V. / Strange, R.W. / Eady, R.R. / Hasnain, S.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystallography with Online Optical and X-Ray Absorption Spectroscopies Demonstrates an Ordered Mechanism in Copper Nitrite Reductase. Authors: Hough, M.A. / Antonyuk, S.V. / Strange, R.W. / 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 | 2vm4.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vm4.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/2vm4 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vm4 | HTTPS FTP |
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-Related structure data
Related structure data | 2vm3C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36570.527 Da / Num. of mol.: 1 / 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 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56.84 % / 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→20.7 Å / Num. obs: 32080 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.5 |
Reflection shell | Highest resolution: 1.9 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.2 / % possible all: 72.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE1 Resolution: 1.9→68.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.84 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.128 / 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: 20.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→68.68 Å
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Refine LS restraints |
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