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

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Basic information

Entry
Database: PDB / ID: 11tt
TitleCrystal structure of apo alpha/beta-hydrolase macrolide esterase EstT from Sphingobacterium thalpophilum (S102A mutant)
Componentsalpha/beta-hydrolase macrolide esterase EstT
KeywordsHYDROLASE / alpha/beta-hydrolase / esterase / macrolide resistance
Function / homology3-oxoadipate enol-lactonase / 3-oxoadipate enol-lactonase activity / glycerolipid catabolic process / : / triacylglycerol lipase activity / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / 3-oxoadipate enol-lactonase 2
Function and homology information
Biological speciesSphingobacterium thalpophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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


Theoretical massNumber of molelcules
Total (without water)32,4051
Polymers32,4051
Non-polymers00
Water1,71195
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)46.778, 74.309, 77.004
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: 32405.465 Da / Num. of mol.: 1 / Mutation: S102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium thalpophilum (bacteria)
Gene: catD_1, NCTC11429_00166 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A4U9U5V9, 3-oxoadipate enol-lactonase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.06 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 9.6, 0.2 MgAc, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.18→29.1 Å / Num. obs: 26538 / % possible obs: 74.85 % / Redundancy: 5.1 % / CC1/2: 0.986 / Net I/σ(I): 8.37
Reflection shellResolution: 2.18→2.23 Å / Num. unique obs: 702 / CC1/2: 0.373 / R split: 1.71

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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: 2.18→29.09 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 2081 10.25 %
Rwork0.1838 --
obs0.1894 20295 74.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 0 95 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072080
X-RAY DIFFRACTIONf_angle_d0.8272834
X-RAY DIFFRACTIONf_dihedral_angle_d14.496728
X-RAY DIFFRACTIONf_chiral_restr0.052322
X-RAY DIFFRACTIONf_plane_restr0.006370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.230.3627500.1972444X-RAY DIFFRACTION27
2.23-2.280.2688740.1999574X-RAY DIFFRACTION37
2.28-2.350.288760.2066668X-RAY DIFFRACTION41
2.35-2.420.2646870.2004797X-RAY DIFFRACTION49
2.42-2.490.26451070.2075947X-RAY DIFFRACTION58
2.49-2.580.27421290.20321099X-RAY DIFFRACTION68
2.58-2.690.32811420.19841261X-RAY DIFFRACTION79
2.69-2.810.25771640.18991379X-RAY DIFFRACTION85
2.81-2.960.27041680.20581465X-RAY DIFFRACTION90
2.96-3.140.24821750.17931542X-RAY DIFFRACTION95
3.14-3.380.23861680.1831609X-RAY DIFFRACTION99
3.38-3.720.19311860.17011597X-RAY DIFFRACTION99
3.72-4.260.21521750.15471618X-RAY DIFFRACTION99
4.26-5.360.20281920.16181605X-RAY DIFFRACTION100
5.37-29.090.24051880.21521609X-RAY DIFFRACTION100

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