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Open data
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Basic information
Entry | Database: PDB / ID: 2bmo | ||||||
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Title | The Crystal Structure of Nitrobenzene Dioxygenase | ||||||
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![]() | OXIDOREDUCTASE / NITROBENZENE DIOXYGENASE / NITROARENE / RIESKE NON-HEME DIOXYGENASE / SUBSTRATE SPECIFICITY IRON-SULFUR / METAL-BINDING / NAD | ||||||
Function / homology | ![]() 3-phenylpropionate catabolic process / : / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Friemann, R. / Ivkovic-Jensen, M.M. / Lessner, D.J. / Yu, C. / Gibson, D.T. / Parales, R.E. / Eklund, H. / Ramaswamy, S. | ||||||
![]() | ![]() Title: Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase. Authors: Friemann, R. / Ivkovic-Jensen, M.M. / Lessner, D.J. / Yu, C.L. / Gibson, D.T. / Parales, R.E. / Eklund, H. / Ramaswamy, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 306.5 KB | Display | ![]() |
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PDB format | ![]() | 247.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.2 KB | Display | ![]() |
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Full document | ![]() | 488 KB | Display | |
Data in XML | ![]() | 34.1 KB | Display | |
Data in CIF | ![]() | 52 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bmqC ![]() 2bmrC ![]() 1o7wS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 49614.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: WASTE TREATMENT PLANT IN NEW JERSEY. (SF NISHINO AND JC SPAIN. 1995. APPL. ENVIRON. MICROBIOL. Plasmid: PDTG927 / Production host: ![]() ![]() |
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#2: Protein | Mass: 23122.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: WASTE TREATMENT PLANT IN NEW JERSEY. (SF NISHINO AND JC SPAIN. 1995. APPL. ENVIRON. MICROBIOL. 61\:2308-2313) Plasmid: PDTG927 / Production host: ![]() ![]() |
-Non-polymers , 6 types, 758 molecules ![](data/chem/img/FES.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/EOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FES / | ||||||
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#4: Chemical | ChemComp-FE / | ||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-EOH / #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.7 % |
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Crystal grow | Details: 0.1M MES PH 6.0, 6% PEG 8000 (W/V), 5MM NICL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 14, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99989 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→52 Å / Num. obs: 207117 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.4 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O7W Resolution: 1.2→52 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.058 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.037 / 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: 16.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→52 Å
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Refine LS restraints |
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