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- PDB-7puj: Crystal structure of Endoglycosidase E GH18 domain from Enterococ... -

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Basic information

Entry
Database: PDB / ID: 7puj
TitleCrystal structure of Endoglycosidase E GH18 domain from Enterococcus faecalis
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / Glycoside hydrolase / GH18 / glycan / antibody / Enterococcus faecalis / EndoE
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / : / carbohydrate metabolic process / membrane
Similarity search - Function
: / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsGarcia-Alija, M. / Du, J.J. / Trastoy, B. / Sundberg, E.J. / Guerin, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI149297 United States
CitationJournal: Nat Commun / Year: 2022
Title: Mechanism of cooperative N-glycan processing by the multi-modular endoglycosidase EndoE.
Authors: Garcia-Alija, M. / Du, J.J. / Ordonez, I. / Diz-Vallenilla, A. / Moraleda-Montoya, A. / Sultana, N. / Huynh, C.G. / Li, C. / Donahue, T.C. / Wang, L.X. / Trastoy, B. / Sundberg, E.J. / Guerin, M.E.
History
DepositionSep 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2957
Polymers48,9621
Non-polymers3336
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-151 kcal/mol
Surface area18640 Å2
Unit cell
Length a, b, c (Å)112.150, 112.150, 64.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Beta-N-acetylhexosaminidase


Mass: 48962.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: ndoE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6U890, beta-N-acetylhexosaminidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20 mM zinc chloride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.752→38.82 Å / Num. obs: 46562 / % possible obs: 99.89 % / Redundancy: 19.1 % / Biso Wilson estimate: 25.47 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06049 / Rrim(I) all: 0.06211 / Net I/σ(I): 34.02
Reflection shellResolution: 1.752→1.815 Å / Redundancy: 13 % / Rmerge(I) obs: 0.9085 / Mean I/σ(I) obs: 2.73 / Num. unique obs: 4569 / CC1/2: 0.839 / CC star: 0.955 / Rrim(I) all: 0.9456 / % possible all: 99.05

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MDV

6mdv


Resolution: 1.752→38.82 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 4561 5 %
Rwork0.1861 --
obs0.1879 46559 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.752→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 6 226 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0243433
X-RAY DIFFRACTIONf_angle_d0.7874669
X-RAY DIFFRACTIONf_dihedral_angle_d5.3062803
X-RAY DIFFRACTIONf_chiral_restr0.049517
X-RAY DIFFRACTIONf_plane_restr0.006615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.752-1.77170.2921420.28752719X-RAY DIFFRACTION95
1.7717-1.79250.28121510.24952919X-RAY DIFFRACTION100
1.7925-1.81440.26781530.24612866X-RAY DIFFRACTION100
1.8144-1.83740.24621550.23912970X-RAY DIFFRACTION100
1.8374-1.86150.25191500.22382843X-RAY DIFFRACTION100
1.8615-1.8870.28311530.21322896X-RAY DIFFRACTION100
1.887-1.9140.25891520.22112895X-RAY DIFFRACTION100
1.914-1.94260.24041520.2142874X-RAY DIFFRACTION100
1.9426-1.97290.2541470.20482883X-RAY DIFFRACTION100
1.9729-2.00530.2591520.20152916X-RAY DIFFRACTION100
2.0053-2.03980.24381530.20652894X-RAY DIFFRACTION100
2.0398-2.07690.24971530.19862905X-RAY DIFFRACTION100
2.0769-2.11690.22441530.19542896X-RAY DIFFRACTION100
2.1169-2.16010.21251570.19472937X-RAY DIFFRACTION100
2.1601-2.20710.24821440.19142814X-RAY DIFFRACTION100
2.2071-2.25840.21831520.19782904X-RAY DIFFRACTION100
2.2584-2.31490.2131580.19922948X-RAY DIFFRACTION100
2.3149-2.37750.24771530.20142873X-RAY DIFFRACTION100
2.3775-2.44740.22031510.19182907X-RAY DIFFRACTION100
2.4474-2.52640.27391510.19152866X-RAY DIFFRACTION100
2.5264-2.61670.25931520.19992888X-RAY DIFFRACTION100
2.6167-2.72140.2641510.19752900X-RAY DIFFRACTION100
2.7214-2.84530.23291520.19622912X-RAY DIFFRACTION100
2.8453-2.99520.22611490.19712888X-RAY DIFFRACTION100
2.9952-3.18280.23171520.18332873X-RAY DIFFRACTION100
3.1828-3.42850.21761530.18692922X-RAY DIFFRACTION100
3.4285-3.77330.18641550.17922876X-RAY DIFFRACTION100
3.7733-4.31890.20441550.14612932X-RAY DIFFRACTION100
4.3189-5.43950.16481520.162867X-RAY DIFFRACTION100
5.4395-38.820.19341580.16912892X-RAY DIFFRACTION100

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