+Open data
-Basic information
Entry | Database: PDB / ID: 7dtq | ||||||
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Title | Apo Crystal Structure of Octaketide Synthase from A. arborescens | ||||||
Components | Octaketide synthase 1 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information flavonoid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Aloe arborescens (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Li, T.L. / Adhikari, K. / Li, Y.S. | ||||||
Citation | Journal: To Be Published Title: Apo Crystal Structure of Octaketide synthase from Aloe arborescens. Authors: Li, T.L. / Adhikari, K. / Li, Y.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dtq.cif.gz | 296.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dtq.ent.gz | 241.5 KB | Display | PDB format |
PDBx/mmJSON format | 7dtq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dtq_validation.pdf.gz | 456.2 KB | Display | wwPDB validaton report |
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Full document | 7dtq_full_validation.pdf.gz | 465.6 KB | Display | |
Data in XML | 7dtq_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 7dtq_validation.cif.gz | 68 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/7dtq ftp://data.pdbj.org/pub/pdb/validation_reports/dt/7dtq | HTTPS FTP |
-Related structure data
Related structure data | 2d3mS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44622.262 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aloe arborescens (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q3L7F5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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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: 2.52 Å3/Da / Density % sol: 51.16 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M sodium potassium tartarate, 0.1M Bistris propane (pH 6.5) 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→25.6 Å / Num. obs: 171608 / % possible obs: 95.31 % / Redundancy: 3.1 % / CC1/2: 0.85 / Net I/σ(I): 2.11 |
Reflection shell | Resolution: 1.75→1.81 Å / Num. unique obs: 171608 / CC1/2: 0.85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D3M Resolution: 1.75→25.6 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.81 / 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: 1.75→25.6 Å
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Refine LS restraints |
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LS refinement shell |
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