[English] 日本語
Yorodumi- PDB-5fal: Crystal structure of PvHCT in complex with CoA and p-coumaroyl-sh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fal | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of PvHCT in complex with CoA and p-coumaroyl-shikimate | ||||||
Components | Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase 2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Panicum virgatum (switchgrass) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.861 Å | ||||||
Authors | Pereira, J.H. / Moriarty, N.W. / Eudes, A. / Yogiswara, S. / Wang, G. / Benites, V.T. / Baidoo, E.E.K. / Lee, T.S. / Keasling, J.D. / Loque, D. / Adams, P.D. | ||||||
Citation | Journal: Plant Cell.Physiol. / Year: 2016 Title: Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin. Authors: Eudes, A. / Pereira, J.H. / Yogiswara, S. / Wang, G. / Teixeira Benites, V. / Baidoo, E.E. / Lee, T.S. / Adams, P.D. / Keasling, J.D. / Loque, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fal.cif.gz | 268.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fal.ent.gz | 218.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fal_validation.pdf.gz | 937.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fal_full_validation.pdf.gz | 938.2 KB | Display | |
Data in XML | 5fal_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 5fal_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/5fal ftp://data.pdbj.org/pub/pdb/validation_reports/fa/5fal | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 48936.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Panicum virgatum (switchgrass) / Production host: Escherichia coli (E. coli) / References: UniProt: R9RYW2 |
---|---|
#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-SKT / ( |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium Sulfate, 0.1 M Tris-HCl pH 8.5 and 25% w/v PEG 3,350 PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99998 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 38682 / % possible obs: 96.1 % / Redundancy: 7.9 % / Net I/σ(I): 14.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.861→49.061 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.21 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.861→49.061 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|