+Open data
-Basic information
Entry | Database: PDB / ID: 6j0z | ||||||
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Title | Crystal structure of AlpK | ||||||
Components | Putative angucycline-like polyketide oxygenase | ||||||
Keywords | OXIDOREDUCTASE / Putative oxygenase / FAD-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces ambofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.889 Å | ||||||
Authors | Wang, W. / Liu, Y. / Liang, H. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Crystal structure of AlpK: An essential monooxygenase involved in the biosynthesis of kinamycin Authors: Wang, W. / Li, J. / Li, H. / Fan, K. / Liu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j0z.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j0z.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 6j0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/6j0z ftp://data.pdbj.org/pub/pdb/validation_reports/j0/6j0z | HTTPS FTP |
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-Related structure data
Related structure data | 4x4jS S: Starting model for refinement |
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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: 52320.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces ambofaciens (bacteria) / Gene: alpK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6VMI4 |
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#2: Chemical | ChemComp-FAD / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.01M magnesium sulfate heptahydrate, 0.1M sodium Cacodylate, 0.8M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.889→29.24 Å / Num. obs: 14697 / % possible obs: 95.01 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.01292 / Net I/σ(I): 25.89 |
Reflection shell | Resolution: 2.889→2.992 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1089 / Mean I/σ(I) obs: 5.58 / Num. unique obs: 1204 / CC1/2: 0.973 / % possible all: 83.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X4J Resolution: 2.889→29.235 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 31.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.889→29.235 Å
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Refine LS restraints |
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