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- PDB-35ym: Structure of an Enterococcus faecium O-glycopeptidase in complex ... -

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Basic information

Entry
Database: PDB / ID: 35ym
TitleStructure of an Enterococcus faecium O-glycopeptidase in complex with the T-antigen
ComponentsEfmM60
KeywordsHYDROLASE / O-glycopeptidase / mucinase / Enterococcus / mucin / O-glycosylation
Function / homologySERINE / :
Function and homology information
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBoraston, A.B. / Mihalynuk, L.G. / Pluvinage, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT 203890 Canada
CitationJournal: To Be Published
Title: Structure of an Enterococcus faecium O-glycopeptidase in complex with the T-antigen
Authors: Boraston, A.B. / Mihalynuk, L.G. / Pluvinage, B.
History
DepositionMay 22, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EfmM60
B: EfmM60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,55112
Polymers119,2172
Non-polymers1,33410
Water9,044502
1
A: EfmM60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2656
Polymers59,6091
Non-polymers6565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EfmM60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2876
Polymers59,6091
Non-polymers6785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.674, 82.406, 84.445
Angle α, β, γ (deg.)70.107, 77.275, 80.304
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein EfmM60


Mass: 59608.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: DTX73_14500 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7V7KSJ4
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 510 molecules

#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NaCl and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. obs: 50563 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.64 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.051 / Net I/σ(I): 13.3
Reflection shellResolution: 2.28→2.34 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1817 / CC1/2: 0.868 / Rpim(I) all: 0.293

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→27.72 Å / SU ML: 0.277 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.5829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2502 2250 4.82 %
Rwork0.1947 44424 -
obs0.1975 46674 91.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.86 Å2
Refinement stepCycle: LAST / Resolution: 2.28→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7852 0 79 502 8433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00198074
X-RAY DIFFRACTIONf_angle_d0.46610932
X-RAY DIFFRACTIONf_chiral_restr0.04121243
X-RAY DIFFRACTIONf_plane_restr0.00271405
X-RAY DIFFRACTIONf_dihedral_angle_d13.79332941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.330.2496940.20251723X-RAY DIFFRACTION57.9
2.33-2.390.27671090.20542100X-RAY DIFFRACTION69.71
2.39-2.450.30461100.21212316X-RAY DIFFRACTION76.82
2.45-2.510.22221100.22322551X-RAY DIFFRACTION83.08
2.51-2.590.31271290.22582807X-RAY DIFFRACTION92.47
2.59-2.670.25011480.22522998X-RAY DIFFRACTION97.98
2.67-2.770.3221560.23032958X-RAY DIFFRACTION99.68
2.77-2.880.28181300.22483075X-RAY DIFFRACTION99.78
2.88-3.010.2861600.23113032X-RAY DIFFRACTION99.84
3.01-3.170.26421380.22353026X-RAY DIFFRACTION99.59
3.17-3.370.30641690.21242983X-RAY DIFFRACTION99.31
3.37-3.620.23651980.19642943X-RAY DIFFRACTION99.12
3.62-3.990.25371630.17242962X-RAY DIFFRACTION97.84
3.99-4.560.23851350.16032982X-RAY DIFFRACTION96.98
4.56-5.740.21111510.16922962X-RAY DIFFRACTION98.39
5.74-27.720.19111500.1773006X-RAY DIFFRACTION99.5

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