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Yorodumi- PDB-2ei3: Anaerobic Crystal Structure Analysis of the 1,2-dihydroxynaphthal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ei3 | ||||||
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Title | Anaerobic Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexes with 2,3-dihydroxybiphenyl | ||||||
Components | 1,2-dihydroxynaphthalene dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / extradiol dioxygenase / protein substrate complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 2ei3.cif.gz | 135.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ei3.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ei3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ei3_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 2ei3_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 2ei3_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 2ei3_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/2ei3 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/2ei3 | HTTPS FTP |
-Related structure data
Related structure data | 2ehzC 2ei0C 2ei2C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33985.559 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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-Non-polymers , 5 types, 209 molecules
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-FE2 / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | BPY 350 AND GOL 902, HOH 903-905 ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER. ABOUT THE LINK ...BPY 350 AND GOL 902, HOH 903-905 ARE IN ALTERNATE CONFORMATI |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.31 % |
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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, anaerobic crystallization, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: focusing mirror optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 26960 / % possible obs: 91.8 % / Redundancy: 4.3 % / Rsym value: 0.058 |
Reflection shell | Highest resolution: 1.9 Å / Rsym value: 0.658 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HAN Resolution: 1.9→28.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.131 / 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: 25.719 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→28.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.899→1.948 Å / Total num. of bins used: 20
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