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Yorodumi- PDB-5kjw: Crystal structure of Coleus blumei HCT in complex with 3-hydroxya... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kjw | ||||||||||||
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Title | Crystal structure of Coleus blumei HCT in complex with 3-hydroxyacetophenone | ||||||||||||
Components | Hydroxycinnamoyl transferase | ||||||||||||
Keywords | TRANSFERASE / phenylpropanoid metabolism / BAHD / HCT / acyltransferase | ||||||||||||
Function / homology | Function and homology information shikimate O-hydroxycinnamoyltransferase / shikimate O-hydroxycinnamoyltransferase activity Similarity search - Function | ||||||||||||
Biological species | Solenostemon scutellarioides (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||||||||
Authors | Levsh, O. / Chiang, Y.C. / Tung, C.F. / Noel, J.P. / Wang, Y. / Weng, J.K. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biochemistry / Year: 2016 Title: Dynamic Conformational States Dictate Selectivity toward the Native Substrate in a Substrate-Permissive Acyltransferase. Authors: Levsh, O. / Chiang, Y.C. / Tung, C.F. / Noel, J.P. / Wang, Y. / Weng, J.K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kjw.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kjw.ent.gz | 157.7 KB | Display | PDB format |
PDBx/mmJSON format | 5kjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kjw_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 5kjw_full_validation.pdf.gz | 457 KB | Display | |
Data in XML | 5kjw_validation.xml.gz | 39.9 KB | Display | |
Data in CIF | 5kjw_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/5kjw ftp://data.pdbj.org/pub/pdb/validation_reports/kj/5kjw | HTTPS FTP |
-Related 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: 47177.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solenostemon scutellarioides (plant) / Gene: cbhct2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: E8ZAP2, shikimate O-hydroxycinnamoyltransferase #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: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Bis-Tris:HCl, 25% PEG 3350, pH 7.5. A soaking drop was prepared with 10% (v/v) of 500 mM 3-hydroxyacetophenone, and 10% (v/v) of 100 mM p-coumaroyl CoA, in reservoir solution. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→53.54 Å / Num. obs: 95145 / % possible obs: 87.7 % / Redundancy: 2.7 % / Net I/σ(I): 5.9 |
-Processing
Software |
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Refinement | Resolution: 1.9→53.537 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.35 / 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: 1.9→53.537 Å
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Refine LS restraints |
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LS refinement shell |
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