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- PDB-11ts: Crystal structure of apo alpha/beta-hydrolase macrolide esterase ... -

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Basic information

Entry
Database: PDB / ID: 11ts
TitleCrystal structure of apo alpha/beta-hydrolase macrolide esterase EstT from Sphingobacterium faecium (S126A mutant)
Componentsalpha/beta-hydrolase macrolide esterase EstT
KeywordsHYDROLASE / alpha/beta-hydrolase / esterase / macrolide resistance
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha/Beta hydrolase fold / hydrolase activity / Macrolide hydrolase EstT
Function and homology information
Biological speciesSphingobacterium faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsHemmings, M.Z. / Blanchet, J. / Kelly, E.T.R. / 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
B: alpha/beta-hydrolase macrolide esterase EstT
C: alpha/beta-hydrolase macrolide esterase EstT
D: alpha/beta-hydrolase macrolide esterase EstT
E: alpha/beta-hydrolase macrolide esterase EstT


Theoretical massNumber of molelcules
Total (without water)175,3945
Polymers175,3945
Non-polymers00
Water25214
1
A: alpha/beta-hydrolase macrolide esterase EstT


Theoretical massNumber of molelcules
Total (without water)35,0791
Polymers35,0791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha/beta-hydrolase macrolide esterase EstT


Theoretical massNumber of molelcules
Total (without water)35,0791
Polymers35,0791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: alpha/beta-hydrolase macrolide esterase EstT


Theoretical massNumber of molelcules
Total (without water)35,0791
Polymers35,0791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: alpha/beta-hydrolase macrolide esterase EstT


Theoretical massNumber of molelcules
Total (without water)35,0791
Polymers35,0791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: alpha/beta-hydrolase macrolide esterase EstT


Theoretical massNumber of molelcules
Total (without water)35,0791
Polymers35,0791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.923, 82.320, 392.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
alpha/beta-hydrolase macrolide esterase EstT


Mass: 35078.855 Da / Num. of mol.: 5 / Mutation: S126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium faecium (bacteria) / Gene: estT, RE431_15605 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0ABU1EVH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: HEPES, PEG 4000

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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: 3.19→29.44 Å / Num. obs: 23461 / % possible obs: 83.56 % / Redundancy: 4.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1317 / Net I/σ(I): 8
Reflection shellResolution: 3.19→3.34 Å / Mean I/σ(I) obs: 2.73 / Num. unique obs: 4512 / CC1/2: 0.694

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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: 3.19→29.44 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2962 1180 5.03 %
Rwork0.2647 --
obs0.2663 23456 83.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9633 0 0 14 9647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079819
X-RAY DIFFRACTIONf_angle_d1.08113379
X-RAY DIFFRACTIONf_dihedral_angle_d6.7581382
X-RAY DIFFRACTIONf_chiral_restr0.061534
X-RAY DIFFRACTIONf_plane_restr0.011752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.340.39051060.31291767X-RAY DIFFRACTION54
3.34-3.510.35161230.30672248X-RAY DIFFRACTION70
3.51-3.730.31931410.27422483X-RAY DIFFRACTION76
3.73-4.020.32171300.26222654X-RAY DIFFRACTION81
4.02-4.420.28891450.23932921X-RAY DIFFRACTION88
4.42-5.060.26631790.24823297X-RAY DIFFRACTION98
5.06-6.360.3111700.28763380X-RAY DIFFRACTION100
6.36-29.440.26391860.25513526X-RAY DIFFRACTION100

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