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Yorodumi- PDB-2ei2: Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxyg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ei2 | ||||||
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Title | Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. stain C18 | ||||||
Components | 1,2-dihydroxynaphthalene dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / extradiol dioxygenase | ||||||
Function / homology | Function and homology information 1,2-dihydroxynaphthalene dioxygenase / 1,2-dihydroxynaphthalene dioxygenase activity / naphthalene catabolic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Neau, D.B. / Kelker, M.S. / Colbert, C.L. / Bolin, J.T. | ||||||
Citation | Journal: To be Published Title: Structural explanation for success and failure in the enzymatic ring-cleavage of 3,4 dihydroxybiphenyl and related PCB metabolites Authors: Neau, D.B. / Kelker, M.S. / Maaroufi, H. / Colbert, C.L. / Eltis, L.D. / Bolin, J.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ei2.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ei2.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ei2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ei2_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
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Full document | 2ei2_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 2ei2_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 2ei2_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/2ei2 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/2ei2 | HTTPS FTP |
-Related structure data
Related structure data | 2ehzC 2ei0C 2ei3C 1hanS 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
#1: Protein | Mass: 33971.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: C18 / Gene: doxg / Plasmid: pHMPVDG / Production host: Pseudomonas putida (bacteria) / Strain (production host): KT2442 References: UniProt: P0A108, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-FE2 / | ||
#4: Chemical | #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: 3.11 Å3/Da / Density % sol: 60.45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M NaCl, 0.1M MgCl2, 0.1M Hepes, naerobic crystallization, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.99 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 7, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→48.97 Å / Num. obs: 46344 / % possible obs: 97.1 % / Redundancy: 9.7 % / Rsym value: 0.088 |
Reflection shell | Highest resolution: 1.69 Å / Rsym value: 0.646 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HAN Resolution: 1.69→48.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.064 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.086 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.756 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→48.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.692→1.736 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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