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Yorodumi- PDB-6lpv: structure of Spermidine hydroxycinnamoyl transferases from Arabid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lpv | ||||||
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Title | structure of Spermidine hydroxycinnamoyl transferases from Arabidopsis thaliana | ||||||
Components | Spermidine hydroxycinnamoyl transferase | ||||||
Keywords | PLANT PROTEIN / Key words: BAHD transferase / phenolamides / spermidine / putrescine / multisite-acylation / molecular mechanism / sequence similarity network | ||||||
Function / homology | Function and homology information spermidine:coumaroyl CoA N-acyltransferase activity / spermidine:caffeoyl CoA N-acyltransferase activity / spermidine:feruloyl CoA N-acyltransferase activity / spermidine hydroxycinnamate conjugate biosynthetic process / spermidine:sinapoyl CoA N-acyltransferase activity / pollen exine formation / pollen development / N-acyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å | ||||||
Authors | Wang, C.Y. / Zhang, P. | ||||||
Citation | Journal: Front Plant Sci / Year: 2020 Title: Structural and Biochemical Insights Into Two BAHD Acyltransferases ( At SHT and At SDT) Involved in Phenolamide Biosynthesis. Authors: Wang, C. / Li, J. / Ma, M. / Lin, Z. / Hu, W. / Lin, W. / Zhang, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lpv.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lpv.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 6lpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lpv_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6lpv_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6lpv_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6lpv_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/6lpv ftp://data.pdbj.org/pub/pdb/validation_reports/lp/6lpv | HTTPS FTP |
-Related structure data
Related structure data | 6lpwC 4g0bS S: Starting model for refinement C: citing same article (ref.) |
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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: 50492.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SHT / Production host: Escherichia coli (E. coli) References: UniProt: O64470, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-SPD / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium sulfate, 0.1M Tris-HCl (pH 8.5), 25% W/V PEG 3350 at 20 |
-Data collection
Diffraction | Mean temperature: 81 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Jan 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→50 Å / Num. obs: 22640 / % possible obs: 99.43 % / Redundancy: 2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.94 |
Reflection shell | Resolution: 2.29→2.37 Å / Num. unique obs: 22640 / CC1/2: 0.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G0B Resolution: 2.297→49.14 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.81 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.55 Å2 / Biso mean: 36.6371 Å2 / Biso min: 7.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.297→49.14 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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