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Yorodumi- PDB-8vcd: Crystal Structure of plant Carboxylesterase 15 bound to SL interm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vcd | ||||||||||||
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Title | Crystal Structure of plant Carboxylesterase 15 bound to SL intermediate | ||||||||||||
Components | Carboxylesterase 15 | ||||||||||||
Keywords | HYDROLASE / Carboxylesterase 15 / CXE15 / Strigolactone | ||||||||||||
Function / homology | Function and homology information strigolactone metabolic process / regulation of secondary shoot formation / carboxylesterase activity / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||||||||
Authors | Palayam, M. / Shabek, N. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural insights into strigolactone catabolism by carboxylesterases reveal a conserved conformational regulation. Authors: Palayam, M. / Yan, L. / Nagalakshmi, U. / Gilio, A.K. / Cornu, D. / Boyer, F.D. / Dinesh-Kumar, S.P. / Shabek, N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vcd.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vcd.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vcd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8vcd_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8vcd_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8vcd_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/8vcd ftp://data.pdbj.org/pub/pdb/validation_reports/vc/8vcd | HTTPS FTP |
-Related structure data
Related structure data | 8vcaC 8vceC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36636.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CXE15, At5g06570, F15M7.10 / Production host: Escherichia coli (E. coli) References: UniProt: Q9FG13, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-VTY / ( | #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: 2.85 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Sodium/Potassium Phosphate pH7.5, 0.1M HEPES pH7.5, 22.5% /v PEG Smear Medium, 10% Glycerol PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.19 Å / Num. obs: 18537 / % possible obs: 100 % / Redundancy: 11.3 % / Rpim(I) all: 0.044 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.3→2.4 Å / Num. unique obs: 1686 / Rpim(I) all: 0.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→48.19 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.65 / 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: 2.32→48.19 Å
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Refine LS restraints |
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LS refinement shell |
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