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- PDB-8zr6: Arabidopsis Carboxyl esterase CXE15 E271Q mutant -

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Basic information

Entry
Database: PDB / ID: 8zr6
TitleArabidopsis Carboxyl esterase CXE15 E271Q mutant
ComponentsStrigolactones hydrolase CXE15
KeywordsHYDROLASE / Strigolactone / catabolic enzyme / CXE15
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: 2.55 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 Carboxyl esterase CXE15 E271Q mutant
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionJun 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Strigolactones hydrolase CXE15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9262
Polymers35,8341
Non-polymers921
Water34219
1
A: Strigolactones hydrolase CXE15
hetero molecules

A: Strigolactones hydrolase CXE15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8534
Polymers71,6692
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6520 Å2
ΔGint-44 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.274, 84.274, 118.253
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 Strigolactones hydrolase CXE15 / Carboxylesterase 15 / AtCXE15


Mass: 35834.379 Da / Num. of mol.: 1 / Mutation: E271Q
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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.26 M Sodium phosphate monobasic monohydrate, 0.14 M Potassium phosphate dibasic, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.55→48.45 Å / Num. obs: 14468 / % possible obs: 99.89 % / Redundancy: 20 % / CC1/2: 0.996 / Net I/σ(I): 9.03
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 1.81 / Num. unique obs: 1411 / CC1/2: 0.58 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMACv5.7refinement
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q9FG13-F1

Resolution: 2.55→48.45 Å / SU B: 20.336 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.471 / ESU R Free: 0.269 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23598 1046 7.2 %RANDOM
Rwork0.20181 ---
obs0.20433 14462 99.97 %-
Displacement parametersBiso mean: 37.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å2-0 Å2
2--0.35 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 6 19 2554
LS refinement shellResolution: 2.55→2.64 Å / % reflection obs: 99.5 %

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