+Open data
-Basic information
Entry | Database: PDB / ID: 8vce | ||||||||||||
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Title | Crystal Structure of plant Carboxylesterase 20 | ||||||||||||
Components | Probable carboxylesterase 120 | ||||||||||||
Keywords | HYDROLASE / Carboxylesterase 20 / CXE20 / Strigolactone | ||||||||||||
Function / homology | 4-hydroxyphenylacetate decarboxylase activity / : / carboxylesterase / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / IMIDAZOLE / Probable carboxylesterase 120 Function and homology information | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 8vce.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vce.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 8vce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vce_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8vce_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8vce_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 8vce_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/8vce ftp://data.pdbj.org/pub/pdb/validation_reports/vc/8vce | HTTPS FTP |
-Related structure data
Related structure data | 8vcaC 8vcdC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36222.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CXE20, At5g62180, MMI9.26 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LVB8, carboxylesterase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.21 Å3/Da / Density % sol: 44.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% w/v PEG8000, 20% v/v Ethylene Glycol, 0.1M Imidazole, 0.03M Sodium Nitrate, 0.03M disodium hydrogen phosphate and 0.03M ammonium sulfate |
-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: Apr 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48 Å / Num. obs: 55388 / % possible obs: 99 % / Redundancy: 12.6 % / Rsym value: 0.035 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.85→1.9 Å / Num. unique obs: 2704 / Rsym value: 0.23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→48 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19 / 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: 1.85→48 Å
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Refine LS restraints |
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LS refinement shell |
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