[English] 日本語
Yorodumi- PDB-5m4o: Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m4o | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with 4-nitrophenol | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE / DIOXYGENASE / CUPIN | ||||||
Function / homology | Function and homology information 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 | Sphingomonas sp. TTNP3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Ferraroni, M. / Da Vela, S. / Scozzafava, A. / Kolvenbach, B. / Corvini, P.F.X. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5m4o.cif.gz | 407.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5m4o.ent.gz | 330.6 KB | Display | PDB format |
PDBx/mmJSON format | 5m4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m4o_validation.pdf.gz | 498.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5m4o_full_validation.pdf.gz | 516.8 KB | Display | |
Data in XML | 5m4o_validation.xml.gz | 78.9 KB | Display | |
Data in CIF | 5m4o_validation.cif.gz | 112.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/5m4o ftp://data.pdbj.org/pub/pdb/validation_reports/m4/5m4o | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-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) Sphingomonas sp. TTNP3 (bacteria) 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) Sphingomonas sp. TTNP3 (bacteria) 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-NPO / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % |
---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→29.7 Å / Num. obs: 112445 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.04 % / Biso Wilson estimate: 33.313 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.161 / Net I/σ(I): 6.54 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→29.697 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.347 / SU ML: 0.22 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.21 / Details: U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.25 Å2 / Biso mean: 33.931 Å2 / Biso min: 11.03 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→29.697 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.101→2.155 Å / Total num. of bins used: 20
|