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- PDB-8vce: Crystal Structure of plant Carboxylesterase 20 -

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Basic information

Entry
Database: PDB / ID: 8vce
TitleCrystal Structure of plant Carboxylesterase 20
ComponentsProbable carboxylesterase 120
KeywordsHYDROLASE / Carboxylesterase 20 / CXE20 / Strigolactone
Function / homology4-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 speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPalayam, M. / Shabek, N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2047396 United States
National Science Foundation (NSF, United States)2139805 United States
Department of Energy (DOE, United States)DE-SC0023158 United States
CitationJournal: 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
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable carboxylesterase 120
B: Probable carboxylesterase 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7066
Polymers72,4442
Non-polymers2624
Water7,026390
1
A: Probable carboxylesterase 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3533
Polymers36,2221
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable carboxylesterase 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3533
Polymers36,2221
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.587, 95.701, 100.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable carboxylesterase 120 / AtCXE20


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 ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→48 Å / Num. obs: 55388 / % possible obs: 99 % / Redundancy: 12.6 % / Rsym value: 0.035 / Net I/σ(I): 23.2
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 2704 / Rsym value: 0.23

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER1.19.2_4158phasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1974 2007 3.63 %
Rwork0.1691 --
obs0.1701 55318 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 18 390 5308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085096
X-RAY DIFFRACTIONf_angle_d1.0276936
X-RAY DIFFRACTIONf_dihedral_angle_d5.641698
X-RAY DIFFRACTIONf_chiral_restr0.06770
X-RAY DIFFRACTIONf_plane_restr0.009902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.27391350.23583621X-RAY DIFFRACTION96
1.9-1.950.29221540.23763762X-RAY DIFFRACTION100
1.95-20.27271340.19233796X-RAY DIFFRACTION100
2-2.070.21731330.18053751X-RAY DIFFRACTION100
2.07-2.140.24051490.17513752X-RAY DIFFRACTION100
2.14-2.230.22271440.17373817X-RAY DIFFRACTION100
2.23-2.330.22541380.19173776X-RAY DIFFRACTION100
2.33-2.450.1811390.15733789X-RAY DIFFRACTION100
2.45-2.610.18771420.1653812X-RAY DIFFRACTION100
2.61-2.810.20561430.16963820X-RAY DIFFRACTION100
2.81-3.090.20061500.17343819X-RAY DIFFRACTION100
3.09-3.540.22461430.16543858X-RAY DIFFRACTION100
3.54-4.460.15331490.14643896X-RAY DIFFRACTION100
4.46-480.15861540.15864042X-RAY DIFFRACTION100

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