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- PDB-11tu: Crystal structure of alpha/beta-hydrolase macrolide esterase EstT... -

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Basic information

Entry
Database: PDB / ID: 11tu
TitleCrystal structure of alpha/beta-hydrolase macrolide esterase EstT from Bacillus cereus (S102A mutant) in complex with linearized tylvalosin
Componentsalpha/beta-hydrolase macrolide esterase EstT
KeywordsHYDROLASE / alpha/beta-hydrolase / esterase / macrolide resistance
Function / homologyglycerolipid catabolic process / : / triacylglycerol lipase activity / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / : / Alpha/beta hydrolase
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKelly, E.T.R. / Blanchet, J. / Berghuis, A.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-162365 Canada
CitationJournal: Biorxiv / Year: 2026
Title: Hydration and hydrolysis define antibiotic resistance conferred by macrolide esterases
Authors: Kelly, E.T.R. / Myziuk, I. / Hemmings, M.Z. / Mulla, Z. / Blanchet, J. / Ruzzini, A. / Berghuis, A.M.
History
DepositionMar 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha/beta-hydrolase macrolide esterase EstT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5702
Polymers31,5061
Non-polymers1,0641
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.492, 72.492, 129.214
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 alpha/beta-hydrolase macrolide esterase EstT


Mass: 31505.625 Da / Num. of mol.: 1 / Mutation: S102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: CN307_07515 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2A9A3A8
#2: Chemical ChemComp-A1DAR / linearized tylvalosin


Mass: 1064.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C53H93NO20 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.5, 0.1 mM MgAc, 12% PSM, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.7→29.51 Å / Num. obs: 72097 / % possible obs: 92.55 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1142 / Net I/σ(I): 17.93
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 2.27 / Num. unique obs: 2899 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.51 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 3468 5.2 %
Rwork0.1777 --
obs0.1789 66743 92.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 74 224 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062175
X-RAY DIFFRACTIONf_angle_d0.8262970
X-RAY DIFFRACTIONf_dihedral_angle_d15.839782
X-RAY DIFFRACTIONf_chiral_restr0.054359
X-RAY DIFFRACTIONf_plane_restr0.006377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.3551790.26311466X-RAY DIFFRACTION53
1.73-1.750.2059890.24781482X-RAY DIFFRACTION56
1.75-1.780.2627920.21561767X-RAY DIFFRACTION64
1.78-1.80.21651070.20281995X-RAY DIFFRACTION72
1.8-1.830.1951290.19652271X-RAY DIFFRACTION84
1.83-1.860.2711250.20012432X-RAY DIFFRACTION89
1.86-1.90.23561480.19442657X-RAY DIFFRACTION97
1.9-1.940.2191510.2042709X-RAY DIFFRACTION100
1.94-1.970.20471530.18782759X-RAY DIFFRACTION100
1.97-2.020.20881490.19672715X-RAY DIFFRACTION100
2.02-2.060.19911470.19272726X-RAY DIFFRACTION100
2.06-2.120.1791510.17512745X-RAY DIFFRACTION100
2.12-2.170.21541480.18882720X-RAY DIFFRACTION100
2.17-2.240.23361510.17672728X-RAY DIFFRACTION100
2.24-2.310.23951480.17712767X-RAY DIFFRACTION100
2.31-2.390.23241500.17572742X-RAY DIFFRACTION100
2.39-2.490.19171490.1792720X-RAY DIFFRACTION100
2.49-2.60.17951500.18622736X-RAY DIFFRACTION100
2.6-2.740.20521500.17562714X-RAY DIFFRACTION100
2.74-2.910.20811500.17812757X-RAY DIFFRACTION100
2.91-3.130.19291470.1692732X-RAY DIFFRACTION100
3.13-3.450.24151460.17782743X-RAY DIFFRACTION100
3.45-3.950.16951460.15162730X-RAY DIFFRACTION100
3.95-4.970.12381550.14262733X-RAY DIFFRACTION100
4.97-29.510.20631580.17872729X-RAY DIFFRACTION100

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