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- PDB-11tw: Crystal structure of alpha/beta-hydrolase macrolide esterase EstX... -

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Basic information

Entry
Database: PDB / ID: 11tw
TitleCrystal structure of alpha/beta-hydrolase macrolide esterase EstX from Escherichia coli (S102A mutant) in complex with linearized tylvalosin
Componentsalpha/beta-hydrolase macrolide esterase EstX
KeywordsHYDROLASE / alpha/beta-hydrolase / esterase / macrolide resistance
Function / homologyglycerolipid catabolic process / : / triacylglycerol lipase activity / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / transferase activity / Alpha/Beta hydrolase fold / : / Aclacinomycin methylesterase RdmC
Function and homology information
Biological speciesEscherichia coli #1/H766 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
D: alpha/beta-hydrolase macrolide esterase EstX
A: alpha/beta-hydrolase macrolide esterase EstX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1813
Polymers62,1162
Non-polymers1,0641
Water3,747208
1
D: alpha/beta-hydrolase macrolide esterase EstX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1222
Polymers31,0581
Non-polymers1,0641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: alpha/beta-hydrolase macrolide esterase EstX


Theoretical massNumber of molelcules
Total (without water)31,0581
Polymers31,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.858, 72.850, 82.329
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha/beta-hydrolase macrolide esterase EstX / EstX / Putative esterase / Streptothricin acetyl transferase / Streptothricin acetyltransferase


Mass: 31058.162 Da / Num. of mol.: 2 / Mutation: S102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli #1/H766 (bacteria) / Gene: estX, rdmC, sat / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q75WM3
#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.: 208 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 mM Bicine pH 9.5, 22% PSB

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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 PILATUS3 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: 1.99→29.04 Å / Num. obs: 33407 / % possible obs: 92.1 % / Redundancy: 2.8 % / CC1/2: 0.986 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.42
Reflection shellResolution: 1.99→2.04 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3419 / CC1/2: 0.7

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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: 1.99→29.04 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 1999 5.98 %
Rwork0.1637 --
obs0.1665 33404 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4285 0 74 208 4567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074484
X-RAY DIFFRACTIONf_angle_d0.8916119
X-RAY DIFFRACTIONf_dihedral_angle_d15.8031626
X-RAY DIFFRACTIONf_chiral_restr0.055694
X-RAY DIFFRACTIONf_plane_restr0.008783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.2196910.15591421X-RAY DIFFRACTION58
2.04-2.10.26651160.1761827X-RAY DIFFRACTION76
2.1-2.160.23421300.1762039X-RAY DIFFRACTION84
2.16-2.230.24451440.16582277X-RAY DIFFRACTION94
2.23-2.310.22581490.16152326X-RAY DIFFRACTION96
2.31-2.40.22671480.1682332X-RAY DIFFRACTION96
2.4-2.510.23291510.16442383X-RAY DIFFRACTION97
2.51-2.640.22761510.172361X-RAY DIFFRACTION97
2.64-2.810.21961500.1662366X-RAY DIFFRACTION98
2.81-3.020.19681520.16992377X-RAY DIFFRACTION98
3.02-3.320.20691530.17192407X-RAY DIFFRACTION98
3.33-3.810.19481540.16022406X-RAY DIFFRACTION98
3.81-4.790.17141540.14232425X-RAY DIFFRACTION99
4.79-29.040.22391560.17272458X-RAY DIFFRACTION98

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