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Yorodumi- PDB-2bmr: The Crystal Structure of Nitrobenzene Dioxygenase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bmr | ||||||
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Title | The Crystal Structure of Nitrobenzene Dioxygenase in complex with 3- nitrotoluene | ||||||
Components |
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Keywords | OXIDOREDUCTASE / NITROBENZENE DIOXYGENASE / NITROARENE / RIESKE NON-HEME DIOXYGENASE / SUBSTRATE SPECIFICITY IRON-SULFUR / METAL-BINDING / NAD | ||||||
Function / homology | Function and homology information 3-phenylpropionate catabolic process / : / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | ||||||
Biological species | COMAMONAS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Friemann, R. / Ivkovic-Jensen, M.M. / Lessner, D.J. / Yu, C. / Gibson, D.T. / Parales, R.E. / Eklund, H. / Ramaswamy, S. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bmr.cif.gz | 166.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bmr.ent.gz | 129.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bmr_validation.pdf.gz | 489.1 KB | Display | wwPDB validaton report |
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Full document | 2bmr_full_validation.pdf.gz | 494.8 KB | Display | |
Data in XML | 2bmr_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 2bmr_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/2bmr ftp://data.pdbj.org/pub/pdb/validation_reports/bm/2bmr | HTTPS FTP |
-Related structure data
Related structure data | 2bmoSC 2bmqC 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 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.) COMAMONAS SP. (bacteria) / Strain: JS765 Description: WASTE TREATMENT PLANT IN NEW JERSEY. (SF NISHINO AND JC SPAIN. 1995. APPL. ENVIRON. MICROBIOL. Plasmid: PDTG927 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q8RTL4 |
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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.) COMAMONAS SP. (bacteria) / Strain: JS765 Description: WASTE TREATMENT PLANT IN NEW JERSEY. (SF NISHINO AND JC SPAIN. 1995. APPL. ENVIRON. MICROBIOL. 61\:2308-2313) Plasmid: PDTG927 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q8RTL3 |
-Non-polymers , 7 types, 747 molecules
#3: Chemical | ChemComp-FES / | ||||||
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#4: Chemical | ChemComp-FE / | ||||||
#5: Chemical | ChemComp-3NT / | ||||||
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-EOH / #8: Chemical | #9: 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: 2.09 Å3/Da / Density % sol: 40.71 % |
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Crystal grow | Details: 0.1M MES PH, 6% PEG 8000 (W/V), 5MM NICL2, 50 MM 3-NITROTOLUENE. THE 3-NITROTOLUENE WAS PREPARED FROM A 1M STOCK SOLUTION WHERE 3-NITROTOLUENE HAS BEEN DISOLVED IN ETHANOL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.08748 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 14, 2004 |
Radiation | Monochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08748 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→60.86 Å / Num. obs: 108450 / % possible obs: 98.7 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BMO Resolution: 1.5→52.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.097 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.07 / 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: 16.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→52.55 Å
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Refine LS restraints |
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