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- PDB-5xbp: Oxygenase component of 3-nitrotoluene dioxygenase from Diaphoroba... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xbp | |||||||||
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Title | Oxygenase component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2 | |||||||||
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![]() | METAL BINDING PROTEIN / Rieske non-heme oxygenase / iron-sulfur clusters / oxidoreductase / nitroaromatic compounds degrader | |||||||||
Function / homology | ![]() : / : / dioxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ramaswamy, S. / Kumari, A. / Singh, D. / Gurunath, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2. Authors: Kumari, A. / Singh, D. / Ramaswamy, S. / Ramanathan, G. #1: ![]() Title: Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2 Authors: Kumari, A. / 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 | ![]() | 379.9 KB | Display | ![]() |
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PDB format | ![]() | 311 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.9 KB | Display | ![]() |
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Full document | ![]() | 527.1 KB | Display | |
Data in XML | ![]() | 68.2 KB | Display | |
Data in CIF | ![]() | 93.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ndoS 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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Unit cell |
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Components
#1: Protein | Mass: 49588.383 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 22951.061 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.14 Å3/Da / Density % sol: 76.06 % / Description: Red orange hexagonal plated sheet |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate tribasic, 18-20% PEG 3350 / PH range: 7.9-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2014 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.711 Å / Num. obs: 95735 / % possible obs: 96.8 % / Redundancy: 5.2 % / CC1/2: 0.984 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.113 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.346 / Num. unique obs: 4714 / Rpim(I) all: 1.043 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NDO Resolution: 2.9→47.711 Å / SU ML: 0.52 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 32.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→47.711 Å
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Refine LS restraints |
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LS refinement shell |
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