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- PDB-8vcd: Crystal Structure of plant Carboxylesterase 15 bound to SL interm... -

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Basic information

Entry
Database: PDB / ID: 8vcd
TitleCrystal Structure of plant Carboxylesterase 15 bound to SL intermediate
ComponentsCarboxylesterase 15
KeywordsHYDROLASE / 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
: / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
(5S)-5-hydroxy-3-methylfuran-2(5H)-one / Strigolactones hydrolase CXE15
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylesterase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9354
Polymers36,6361
Non-polymers2983
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.340, 84.340, 117.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Carboxylesterase 15 / AtCXE15 / Strigolactones hydrolase CXE15


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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VTY / (5S)-5-hydroxy-3-methylfuran-2(5H)-one


Mass: 114.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.85 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 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

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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: Oct 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.3→2.4 Å / Num. unique obs: 1686 / Rpim(I) all: 0.33

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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: 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
RfactorNum. reflection% reflection
Rfree0.2288 1854 10 %
Rwork0.1885 --
obs0.1926 18535 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 20 54 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032621
X-RAY DIFFRACTIONf_angle_d0.5363553
X-RAY DIFFRACTIONf_dihedral_angle_d5.194355
X-RAY DIFFRACTIONf_chiral_restr0.041381
X-RAY DIFFRACTIONf_plane_restr0.005465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.33721360.24941224X-RAY DIFFRACTION95
2.38-2.450.29811330.21521200X-RAY DIFFRACTION94
2.45-2.530.27921380.20381246X-RAY DIFFRACTION96
2.53-2.620.27851380.21661232X-RAY DIFFRACTION96
2.62-2.730.26031390.21441261X-RAY DIFFRACTION97
2.73-2.850.29191410.21991256X-RAY DIFFRACTION98
2.85-30.26231430.18661287X-RAY DIFFRACTION98
3-3.190.2481400.18351267X-RAY DIFFRACTION99
3.19-3.440.23111440.1811296X-RAY DIFFRACTION99
3.44-3.780.18381460.1811313X-RAY DIFFRACTION99
3.78-4.330.23051460.17121312X-RAY DIFFRACTION99
4.33-5.450.19441500.1691348X-RAY DIFFRACTION99
5.45-48.190.19181600.19181439X-RAY DIFFRACTION99

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