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- PDB-8zrf: Arabidopsis Carboxylesterase CXE15 -

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Basic information

Entry
Database: PDB / ID: 8zrf
TitleArabidopsis Carboxylesterase CXE15
ComponentsCarboxylesterase 15
KeywordsHYDROLASE / CXE15 / carboxylesterase / catabolic enzyme / strigolactones
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: 2.05 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other private Saudi Arabia
CitationJournal: To Be Published
Title: Arabidopsis Carboxylesterase CXE15
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: Carboxylesterase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0203
Polymers35,8351
Non-polymers1842
Water90150
1
A: Carboxylesterase 15
hetero molecules

A: Carboxylesterase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0396
Polymers71,6712
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7180 Å2
ΔGint-45 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.091, 84.091, 117.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 35835.363 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-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.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
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: 2.05→48.13 Å / Num. obs: 27053 / % possible obs: 99.82 % / Redundancy: 14 % / Biso Wilson estimate: 46.73 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.37
Reflection shellResolution: 2.05→2.12 Å / Mean I/σ(I) obs: 2.04 / Num. unique obs: 2637 / CC1/2: 0.82 / % possible all: 99.92

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Processing

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

Resolution: 2.05→48.13 Å / SU B: 4.144 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22988 1365 5 %RANDOM
Rwork0.20184 ---
obs0.20326 27041 99.99 %-
Displacement parametersBiso mean: 42.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 12 50 2591
LS refinement shellResolution: 2.05→2.12 Å
RfactorNum. reflection% reflection
Rfree0.2716 --
Rwork0.2675 --
obs-2637 99.92 %

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