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- PDB-7pul: Crystal structure of Endoglycosidase E GH20 domain from Enterococ... -

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Basic information

Entry
Database: PDB / ID: 7pul
TitleCrystal structure of Endoglycosidase E GH20 domain from Enterococcus faecalis
Components
  • Beta-N-acetylhexosaminidase
  • GLY-ALA-GLY-ALA-ALA
KeywordsHYDROLASE / Glycoside hydrolase / GH18 / glycan / antibody / Enterococcus faecalis / EndoE
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / beta-N-acetylhexosaminidase activity / carbohydrate metabolic process / membrane
Similarity search - Function
: / Endo-beta-N-acetylglucosaminidase EndoS TIM-barrel domain / : / 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. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...: / Endo-beta-N-acetylglucosaminidase EndoS TIM-barrel domain / : / 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. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGarcia-Alija, M. / Du, J.J. / Trastoy, B. / Sundberg, E.J. / Guerin, M.
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
P: GLY-ALA-GLY-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3656
Polymers40,2522
Non-polymers1134
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-40 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.298, 57.046, 69.525
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-N-acetylhexosaminidase


Mass: 39906.418 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: Protein/peptide GLY-ALA-GLY-ALA-ALA


Mass: 345.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM bicine/Trizma base pH 8.5, 30 mM magnesium chloride hexahydrate, 30 mM calcium chloride dihydrate, 12.5% w/v PEG 1000, 12.5% PEG w/v 3350, 12.5% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.4→44.08 Å / Num. obs: 60346 / % possible obs: 99.69 % / Redundancy: 3.2 % / Biso Wilson estimate: 12.65 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.07721 / Rrim(I) all: 0.09335 / Net I/σ(I): 11.92
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2442 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 6021 / CC1/2: 0.894 / CC star: 0.971 / Rrim(I) all: 0.2952 / % possible all: 99.52

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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: 3RPM

3rpm


Resolution: 1.4→44.077 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1829 3047 5.05 %
Rwork0.1578 --
obs0.1591 60320 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→44.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 4 309 3092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0412894
X-RAY DIFFRACTIONf_angle_d0.9453904
X-RAY DIFFRACTIONf_dihedral_angle_d13.7821038
X-RAY DIFFRACTIONf_chiral_restr0.077405
X-RAY DIFFRACTIONf_plane_restr0.006514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.42190.24231370.20412604X-RAY DIFFRACTION99
1.4219-1.44520.25161350.19492574X-RAY DIFFRACTION100
1.4452-1.47010.2331320.18442614X-RAY DIFFRACTION100
1.4701-1.49690.20451260.18452575X-RAY DIFFRACTION100
1.4969-1.52560.21471540.17032564X-RAY DIFFRACTION100
1.5256-1.55680.19111500.17152585X-RAY DIFFRACTION100
1.5568-1.59060.19171170.16562597X-RAY DIFFRACTION99
1.5906-1.62760.16871210.16012637X-RAY DIFFRACTION100
1.6276-1.66840.18281350.16072576X-RAY DIFFRACTION100
1.6684-1.71350.171460.16512590X-RAY DIFFRACTION100
1.7135-1.76390.16441370.15892585X-RAY DIFFRACTION100
1.7639-1.82080.1911280.16142610X-RAY DIFFRACTION100
1.8208-1.88590.18711510.15942586X-RAY DIFFRACTION100
1.8859-1.96140.2091460.16172596X-RAY DIFFRACTION100
1.9614-2.05070.1911450.15932582X-RAY DIFFRACTION100
2.0507-2.15880.19221310.15542630X-RAY DIFFRACTION100
2.1588-2.2940.17391450.15292590X-RAY DIFFRACTION100
2.294-2.47110.16561290.15022646X-RAY DIFFRACTION100
2.4711-2.71980.17651430.15192592X-RAY DIFFRACTION100
2.7198-3.11330.17871660.16032606X-RAY DIFFRACTION100
3.1133-3.9220.171360.15062641X-RAY DIFFRACTION100
3.922-44.0770.17641370.14862693X-RAY DIFFRACTION100

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