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Yorodumi- PDB-4p9g: Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p9g | ||||||
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Title | Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. | ||||||
Components | 2,4'-dihydroxyacetophenone dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / Dioxygenase / cupin-fold / iron-binding / carbonate | ||||||
Function / homology | Function and homology information 2,4'-dihydroxyacetophenone dioxygenase / 2,4'-dihydroxyacetophenone dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Keegan, R. / Lebedev, A. / Erskine, P. / Guo, J. / Wood, S.P. / Hopper, D.J. / Cooper, J.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP Authors: Keegan, R. / Lebedev, A. / Erskine, P. / Guo, J. / Wood, S.P. / Hopper, D.J. / Rigby, S.E.J. / Cooper, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p9g.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p9g.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 4p9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p9g_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 4p9g_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 4p9g_validation.xml.gz | 10 KB | Display | |
Data in CIF | 4p9g_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/4p9g ftp://data.pdbj.org/pub/pdb/validation_reports/p9/4p9g | HTTPS FTP |
-Related 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: 22690.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The N-terminal portion could not be defined in the electron density map. Source: (gene. exp.) Alcaligenes sp. (bacteria) / Gene: dad / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9REI7, 2,4'-dihydroxyacetophenone dioxygenase |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CO3 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 56 % / Description: Needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution: protein concentration = 5 mg/ml in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM beta-mercaptoethanol. Chymotrypsin was added in a 1:50 mass-ratio prior to setting up hanging-drop ...Details: Protein solution: protein concentration = 5 mg/ml in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM beta-mercaptoethanol. Chymotrypsin was added in a 1:50 mass-ratio prior to setting up hanging-drop crystallisation trials. Well solution: 10 % w/v PEG 1k and 10 % PEG 10k (Molecular Dimensions Structure Screen 2, condition 46). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.072 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→57 Å / Num. obs: 10549 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.1 / % possible all: 49.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ebr, 2oq1, 3bal, 3cjx Resolution: 2.2→71.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.732 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.697 Å2
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Refine analyze | Luzzati sigma a obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→71.5 Å
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Refine LS restraints |
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