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

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Basic information

Entry
Database: PDB / ID: 7puk
TitleCrystal structure of Endoglycosidase E GH18 domain from Enterococcus faecalis in complex with Man5 product
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: 2.69 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

Downloads & links

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Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9894
Polymers97,9252
Non-polymers2,0642
Water00
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9942
Polymers48,9621
Non-polymers1,0321
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9942
Polymers48,9621
Non-polymers1,0321
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)222.030, 54.550, 83.920
Angle α, β, γ (deg.)90.00, 110.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-N-acetylhexosaminidase


Mass: 48962.340 Da / Num. of mol.: 2
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: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1031.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3-3-3/a4-b1_b3-c1_b6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
Has ligand of interestY

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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, sitting drop
Details: 100 mM Bis-Tris propane pH 6.5, 200 mM sodium nitrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.69→45.73 Å / Num. obs: 26261 / % possible obs: 98.75 % / Redundancy: 4.4 % / Biso Wilson estimate: 62.82 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1232 / Rrim(I) all: 0.1415 / Net I/σ(I): 10.16
Reflection shellResolution: 2.69→2.786 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.8459 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2438 / CC1/2: 0.678 / CC star: 0.899 / Rrim(I) all: 0.9717 / % possible all: 92.8

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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: 7PUJ

7puj


Resolution: 2.69→45.73 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 0.7 / Phase error: 31.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2621 2497 4.99 %
Rwork0.2256 --
obs0.2275 26247 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 0 140 0 6781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026940
X-RAY DIFFRACTIONf_angle_d0.5019476
X-RAY DIFFRACTIONf_dihedral_angle_d13.934174
X-RAY DIFFRACTIONf_chiral_restr0.0361094
X-RAY DIFFRACTIONf_plane_restr0.0031211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.74160.49551180.44282270X-RAY DIFFRACTION83
2.7416-2.79760.41121390.37072645X-RAY DIFFRACTION98
2.7976-2.85840.42161440.36642705X-RAY DIFFRACTION98
2.8584-2.92490.32741390.32392614X-RAY DIFFRACTION99
2.9249-2.9980.3441450.30522692X-RAY DIFFRACTION98
2.998-3.0790.33281380.30882656X-RAY DIFFRACTION99
3.079-3.16960.3511410.29612640X-RAY DIFFRACTION99
3.1696-3.27190.33341370.29222688X-RAY DIFFRACTION99
3.2719-3.38880.29041400.27842658X-RAY DIFFRACTION98
3.3888-3.52440.34251370.25062643X-RAY DIFFRACTION97
3.5244-3.68480.32711400.24242643X-RAY DIFFRACTION97
3.6848-3.87890.25651370.22452633X-RAY DIFFRACTION98
3.8789-4.12180.24771380.1962664X-RAY DIFFRACTION98
4.1218-4.43980.20981370.17112657X-RAY DIFFRACTION98
4.4398-4.88620.21951390.16842685X-RAY DIFFRACTION99
4.8862-5.59210.21871490.18482684X-RAY DIFFRACTION99
5.5921-7.04140.21741390.20342671X-RAY DIFFRACTION99
7.0414-45.730.17711400.17372678X-RAY DIFFRACTION99

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