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- PDB-8vca: Crystal Structure of plant Carboxylesterase 15 -

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Basic information

Entry
Database: PDB / ID: 8vca
TitleCrystal Structure of plant Carboxylesterase 15
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
Strigolactones hydrolase CXE15
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 13, 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: Carboxylesterase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9134
Polymers36,6361
Non-polymers2763
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.915, 83.915, 117.177
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 BL21 (bacteria)
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.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.82 Å3/Da / Density % sol: 56.31 %
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: 7-7.5

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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: Sep 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.04 Å / Num. obs: 19200 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rpim(I) all: 0.049 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 41114 / Rpim(I) all: 0.397

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.04 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 1920 10 %
Rwork0.2004 --
obs0.2044 19196 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 18 48 2581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022612
X-RAY DIFFRACTIONf_angle_d0.5243535
X-RAY DIFFRACTIONf_dihedral_angle_d7.401356
X-RAY DIFFRACTIONf_chiral_restr0.039379
X-RAY DIFFRACTIONf_plane_restr0.004461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.37941330.2511196X-RAY DIFFRACTION100
2.36-2.420.29591330.22991204X-RAY DIFFRACTION100
2.42-2.490.26391350.22551213X-RAY DIFFRACTION100
2.49-2.570.26571350.22211213X-RAY DIFFRACTION100
2.57-2.670.28641340.23311205X-RAY DIFFRACTION100
2.67-2.770.27761360.24021221X-RAY DIFFRACTION100
2.77-2.90.26521360.23041219X-RAY DIFFRACTION100
2.9-3.050.28491340.22611220X-RAY DIFFRACTION100
3.05-3.240.25831370.21681226X-RAY DIFFRACTION100
3.24-3.490.25861380.21131234X-RAY DIFFRACTION100
3.49-3.850.22271370.18261237X-RAY DIFFRACTION100
3.85-4.40.2021390.16521258X-RAY DIFFRACTION100
4.4-5.540.20191420.16771279X-RAY DIFFRACTION100
5.55-48.040.20211510.18981351X-RAY DIFFRACTION100

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