+Open data
-Basic information
Entry | Database: PDB / ID: 5f9p | ||||||
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Title | Crystal structure study of anthrone oxidase-like protein | ||||||
Components | Anthrone oxidase-like protein | ||||||
Keywords | OXIDOREDUCTASE / anthrone oxidase-like protein / oxidative ring-B opening / activity site | ||||||
Function / homology | Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Dimeric alpha-beta barrel / Anthrone oxidase-like protein Function and homology information | ||||||
Biological species | Streptomyces ambofaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.078 Å | ||||||
Authors | Gao, X. / Wu, D. / Fan, K. / Liu, Z.-J. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Structure and Function of a C-C Bond Cleaving Oxygenase in Atypical Angucycline Biosynthesis Authors: Pan, G. / Gao, X. / Fan, K. / Liu, J. / Meng, B. / Gao, J. / Wang, B. / Zhang, C. / Han, H. / Ai, G. / Chen, Y. / Wu, D. / Liu, Z.J. / Yang, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f9p.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f9p.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 5f9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f9p_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 5f9p_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 5f9p_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5f9p_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/5f9p ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f9p | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26746.357 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces ambofaciens (bacteria) / Gene: alpJ, DSMT0187 / Plasmid: pET-30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q6VMI5 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.56 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 1.4M sodium citrate tribasic dehydrate |
-Data collection
Diffraction | Mean temperature: 77.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.078→40.525 Å / Num. obs: 26423 / % possible obs: 100 % / Redundancy: 22.8 % / Net I/σ(I): 5.71 |
Reflection shell | Resolution: 2.078→2.152 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.078→40.515 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.078→40.515 Å
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Refine LS restraints |
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LS refinement shell |
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