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- PDB-8zro: Arabidopsis Carboxylesterase CXE15 -

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Basic information

Entry
Database: PDB / ID: 8zro
TitleArabidopsis Carboxylesterase CXE15
ComponentsStrigolactones hydrolase CXE15
KeywordsHYDROLASE / Catabolic enzyme / CXE15 / strigolactoone / carboxylesterase
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: 3.09 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technology Saudi Arabia
CitationJournal: To Be Published
Title: Arabidopsis Carboxylesterase CXE15
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Strigolactones hydrolase CXE15
B: Strigolactones hydrolase CXE15


Theoretical massNumber of molelcules
Total (without water)71,6712
Polymers71,6712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-4 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.399, 99.399, 114.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 35835.363 Da / Num. of mol.: 2
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9FG13, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 MSodium acetate trihydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.09→49.75 Å / Num. obs: 8670 / % possible obs: 98.2 % / Redundancy: 19.2 % / CC1/2: 0.998 / Net I/σ(I): 14.7
Reflection shellResolution: 3.09→3.3 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 202 / CC1/2: 0.5 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q9FG13-F1

Resolution: 3.09→49.7 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 40.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3387 867 10 %RANDOM
Rwork0.2782 ---
obs0.2841 8666 70.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→49.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 0 0 4766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054889
X-RAY DIFFRACTIONf_angle_d1.0486630
X-RAY DIFFRACTIONf_dihedral_angle_d5.837652
X-RAY DIFFRACTIONf_chiral_restr0.056709
X-RAY DIFFRACTIONf_plane_restr0.009871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.280.4212380.3827347X-RAY DIFFRACTION19
3.28-3.540.3786670.3642618X-RAY DIFFRACTION34
3.54-3.890.39291290.34631197X-RAY DIFFRACTION65
3.89-4.450.37242060.30491828X-RAY DIFFRACTION100
4.46-5.610.32282130.27861866X-RAY DIFFRACTION100
5.61-49.70.31242140.24071943X-RAY DIFFRACTION100

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