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Yorodumi- PDB-4icy: Tracing the Evolution of Angucyclinone Monooxygenases: Structural... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4icy | ||||||
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Title | Tracing the Evolution of Angucyclinone Monooxygenases: Structural Determinants for C-12b Hydroxylation and Substrate Inhibition in PgaE | ||||||
Components | Polyketide oxygenase PgaE | ||||||
Keywords | OXIDOREDUCTASE / FAD-dependent aromatic hydroxylation / monooxygenase / FAD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces sp. PGA64 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kallio, P. / Patrikainen, P. / Belogurov, G. / Mantsala, P. / Yang, K. / Niemi, J. / Metsa-Ketela, M. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Tracing the Evolution of Angucyclinone Monooxygenases: Structural Determinants for C-12b Hydroxylation and Substrate Inhibition in PgaE. Authors: Kallio, P. / Patrikainen, P. / Belogurov, G.A. / Mantsala, P. / Yang, K. / Niemi, J. / Metsa-Ketela, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4icy.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4icy.ent.gz | 151.9 KB | Display | PDB format |
PDBx/mmJSON format | 4icy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/4icy ftp://data.pdbj.org/pub/pdb/validation_reports/ic/4icy | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53623.562 Da / Num. of mol.: 1 / Mutation: P78Q, I79F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. PGA64 (bacteria) / Strain: PGA64 / Gene: pgaE / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q93LY7 |
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-Non-polymers , 6 types, 124 molecules
#2: Chemical | ChemComp-FAD / | ||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 2.0M ammonium sulphate, 0.1M MES-buffer, 2% V/V 1,4-dioxane, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.5 Å / Num. all: 23686 / Num. obs: 23686 / % possible obs: 99.5 % |
Reflection shell | Resolution: 2.4→2.53 Å / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: native PgaE Resolution: 2.4→46.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.922 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.256 / 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: 58.552 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→46.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 28.831 Å / Origin y: 25.3657 Å / Origin z: 26.5758 Å
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