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- PDB-8zrg: Arabidopsis Carboxylesterase CXE15 C14S mutant -

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Basic information

Entry
Database: PDB / ID: 8zrg
TitleArabidopsis Carboxylesterase CXE15 C14S mutant
ComponentsStrigolactones hydrolase CXE15
KeywordsHYDROLASE / Catabolic enzyme / strigolactoone / Carboxylesterase / 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: 2.75 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 C14S mutant
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionJun 4, 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

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Assembly

Deposited unit
A: Strigolactones hydrolase CXE15


Theoretical massNumber of molelcules
Total (without water)35,2771
Polymers35,2771
Non-polymers00
Water52229
1
A: Strigolactones hydrolase CXE15

A: Strigolactones hydrolase CXE15


Theoretical massNumber of molelcules
Total (without water)70,5542
Polymers70,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5630 Å2
ΔGint-27 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.815, 83.815, 120.888
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: 35276.762 Da / Num. of mol.: 1 / Mutation: C14S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2

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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: May 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.75→49.07 Å / Num. obs: 12939 / % possible obs: 99.98 % / Redundancy: 20 % / CC1/2: 0.998 / Net I/σ(I): 12.26
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 15 % / Mean I/σ(I) obs: 1.91 / Num. unique obs: 924 / CC1/2: 0.561 / % possible all: 91.27

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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: 2.75→49.07 Å / SU B: 13.015 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 1.2 / ESU R Free: 0.315 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22537 972 8.5 %RANDOM
Rwork0.17665 ---
obs0.18097 10510 97.7 %-
Displacement parametersBiso mean: 64.469 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.75→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 0 29 2520
LS refinement shellResolution: 2.75→2.85 Å /
Num. reflection% reflection
Rwork924 -
obs-91.27 %

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