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Yorodumi- PDB-3hpv: Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hpv | ||||||
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Title | Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28 | ||||||
Components | Catechol 2,3-dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Repeated motifs / Aromatic hydrocarbons catabolism / Dioxygenase / Iron | ||||||
Function / homology | Function and homology information catechol 2,3-dioxygenase / catechol 2,3-dioxygenase activity / catabolic process / ferrous iron binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Cho, J.-H. / Rhee, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas Authors: Cho, J.-H. / Jung, D.-K. / Lee, K. / Rhee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hpv.cif.gz | 242.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hpv.ent.gz | 196.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hpv_validation.pdf.gz | 467.2 KB | Display | wwPDB validaton report |
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Full document | 3hpv_full_validation.pdf.gz | 511 KB | Display | |
Data in XML | 3hpv_validation.xml.gz | 49.8 KB | Display | |
Data in CIF | 3hpv_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpv ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpv | HTTPS FTP |
-Related structure data
Related structure data | 3hpyC 3hq0C 1mpyS 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
#1: Protein | Mass: 35122.609 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: KL28 / Gene: Pseudomonas sp. KL28 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WYF5, catechol 2,3-dioxygenase #2: Chemical | ChemComp-FE2 / #3: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.71 % / Mosaicity: 0.759 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium fluoride, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23983 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2007 |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23983 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 55382 / Num. obs: 46741 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Redundancy: 13 % / Rmerge(I) obs: 0.119 / Χ2: 1.009 / Net I/σ(I): 23.294 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5478 / Χ2: 0.952 / % possible all: 99.4 |
-Phasing
Phasing | Method: molecular replacement | ||||||||||||
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Phasing MR | Cor.coef. Fo:Fc: 0.749 / Packing: 0.62
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MPY Resolution: 2.3→44.71 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: using a random selection of data / σ(F): 2
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Displacement parameters | Biso max: 81.5 Å2 / Biso mean: 30.416 Å2 / Biso min: 4.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å |