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Yorodumi- PDB-2xsr: Crystal structure of wild type Acinetobacter radioresistens catec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xsr | ||||||
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Title | Crystal structure of wild type Acinetobacter radioresistens catechol 1,2 dioxygenase | ||||||
Components | CATECHOL 1,2 DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / LIPID | ||||||
Function / homology | Function and homology information catechol-containing compound catabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / beta-ketoadipate pathway / ferric iron binding Similarity search - Function | ||||||
Biological species | ACINETOBACTER RADIORESISTENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Micalella, C. / Martignon, S. / Bruno, S. / Rizzi, M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2011 Title: X-Ray Crystallography, Mass Spectrometry and Single Crystal Microspectrophotometry: A Multidisciplinary Characterization of Catechol 1,2 Dioxygenase. Authors: Micalella, C. / Martignon, S. / Bruno, S. / Pioselli, B. / Caglio, R. / Valetti, F. / Pessione, E. / Giunta, C. / Rizzi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xsr.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xsr.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xsr_validation.pdf.gz | 812.3 KB | Display | wwPDB validaton report |
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Full document | 2xsr_full_validation.pdf.gz | 817.2 KB | Display | |
Data in XML | 2xsr_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 2xsr_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/2xsr ftp://data.pdbj.org/pub/pdb/validation_reports/xs/2xsr | HTTPS FTP |
-Related structure data
Related structure data | 2xsuC 2xsvC 2azqS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 34412.188 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-306 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACINETOBACTER RADIORESISTENS (bacteria) Strain: LMG S13 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F103 |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-PIE / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | PHOSHOLIPI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.96 % / Description: NONE |
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Crystal grow | Temperature: 277 K Details: 2 M AMMONIUM SULPHATE, 0.1 M TRIS- HCL PH 8.5, 277K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.981 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 61576 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AZQ Resolution: 1.8→37.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.724 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.094 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.615 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→37.48 Å
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Refine LS restraints |
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