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- PDB-5m21: Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m21 | ||||||
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Title | Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 with 4-hydroxybenzoate bound | ||||||
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![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferraroni, M. / Da Vela, S. / Scozzafava, A. / Kolvenbach, B. / Corvini, P.F.X. | ||||||
![]() | ![]() Title: The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes. Authors: Ferraroni, M. / Da Vela, S. / Kolvenbach, B.A. / Corvini, P.F. / Scozzafava, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 413.2 KB | Display | ![]() |
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PDB format | ![]() | 332.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.5 KB | Display | ![]() |
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Full document | ![]() | 518.5 KB | Display | |
Data in XML | ![]() | 81.8 KB | Display | |
Data in CIF | ![]() | 117 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m22C ![]() 5m26C ![]() 5m4oC ![]() 4zxaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18571.809 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Hydroquinone 1,2-dioxygenase small subunit / Source: (natural) ![]() References: UniProt: F8TW82, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #2: Protein | Mass: 38238.789 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Hydroquinone 1,2-dioxygenase large subunit / Source: (natural) ![]() References: UniProt: F8TW83, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-PHB / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.44 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6.5 / Details: 14% PEG 3350, 0.35 M MgCl2 and 0.1 M Mes |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.99→29.856 Å / Num. obs: 130301 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.32 % / Biso Wilson estimate: 30.103 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.86 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZXA Resolution: 1.99→29.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.872 / SU ML: 0.157 / SU R Cruickshank DPI: 0.1968 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.181 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.29 Å2 / Biso mean: 27.432 Å2 / Biso min: 11.16 Å2
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Refinement step | Cycle: final / Resolution: 1.99→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.994→2.046 Å / Total num. of bins used: 20
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