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- PDB-9fym: Lacto-N-biosidase from Treponema denticola ATCC 35405 -

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Basic information

Entry
Database: PDB / ID: 9fym
TitleLacto-N-biosidase from Treponema denticola ATCC 35405
ComponentsGlycoside hydrolase family 20 catalytic domain-containing protein
KeywordsHYDROLASE / lacto-N-biosidase / GH20
Function / homologyHexosaminidase D-like / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / beta-N-acetylglucosaminidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / IMIDAZOLE / Glycoside hydrolase family 20 catalytic domain-containing protein
Function and homology information
Biological speciesTreponema denticola ATCC 35405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsVuillemin, M. / Siebenhaar, S. / Zeuner, B. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Independent Research Fund Denmark - Technology and Production Sciences9068-00006B Denmark
CitationJournal: Chembiochem / Year: 2025
Title: Discovery of Lacto-N-Biosidases and a Novel N-Acetyllactosaminidase Activity in the CAZy Family GH20: Functional Diversity and Structural Insights.
Authors: Vuillemin, M. / Muschiol, J. / Zhang, Y. / Holck, J. / Barrett, K. / Preben Morth, J. / Meyer, A.S. / Zeuner, B.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside hydrolase family 20 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0626
Polymers37,8161
Non-polymers2465
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Run as monomeric unit on gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.954, 50.701, 153.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glycoside hydrolase family 20 catalytic domain-containing protein


Mass: 37816.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Signal peptide has been removed, additional GS (from Thrombin cleavage).
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Gene: TDE_1723 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73LY9
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% w/v PEG 8000, 9% ethylene glycol, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.34→48.15 Å / Num. obs: 77556 / % possible obs: 99.58 % / Redundancy: 8.2 % / Biso Wilson estimate: 17.71 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.08324 / Rpim(I) all: 0.03112 / Rrim(I) all: 0.08909 / Net I/σ(I): 11.31
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 7469 / CC1/2: 0.464 / Rpim(I) all: 1 / Rrim(I) all: 1 / % possible all: 97.97

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→48.15 Å / SU ML: 0.175 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 7353 4.99 %
Rwork0.1688 140024 -
obs0.1702 73688 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.93 Å2
Refinement stepCycle: LAST / Resolution: 1.34→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 9 352 2958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01422778
X-RAY DIFFRACTIONf_angle_d1.27033772
X-RAY DIFFRACTIONf_chiral_restr0.0905403
X-RAY DIFFRACTIONf_plane_restr0.0127488
X-RAY DIFFRACTIONf_dihedral_angle_d6.0312380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.39292700.37414426X-RAY DIFFRACTION96.45
1.36-1.370.382660.35674712X-RAY DIFFRACTION98.3
1.37-1.390.31862250.33624544X-RAY DIFFRACTION98.86
1.39-1.410.35152440.33214672X-RAY DIFFRACTION99.09
1.41-1.430.31132210.3174715X-RAY DIFFRACTION99.38
1.43-1.450.32612650.30084609X-RAY DIFFRACTION99.51
1.45-1.470.27752230.28854716X-RAY DIFFRACTION99.5
1.47-1.490.26932230.27114703X-RAY DIFFRACTION99.64
1.49-1.510.26252120.25514724X-RAY DIFFRACTION99.72
1.51-1.540.25672730.24254627X-RAY DIFFRACTION99.65
1.54-1.560.23292730.23074650X-RAY DIFFRACTION99.82
1.56-1.590.24043120.22284603X-RAY DIFFRACTION99.72
1.59-1.620.23482410.21034658X-RAY DIFFRACTION99.84
1.62-1.660.22852530.20564665X-RAY DIFFRACTION99.7
1.66-1.690.23812090.20564779X-RAY DIFFRACTION99.62
1.69-1.730.24272500.19234606X-RAY DIFFRACTION99.65
1.73-1.770.23472370.19264685X-RAY DIFFRACTION99.86
1.77-1.820.20682370.17974728X-RAY DIFFRACTION99.78
1.82-1.880.21122490.17344653X-RAY DIFFRACTION100
1.88-1.940.21572470.16584709X-RAY DIFFRACTION99.94
1.94-2.010.19942460.1584692X-RAY DIFFRACTION99.94
2.01-2.090.1712130.15154723X-RAY DIFFRACTION99.88
2.09-2.180.16812180.14994690X-RAY DIFFRACTION99.82
2.18-2.30.16942670.14264674X-RAY DIFFRACTION99.84
2.3-2.440.16572400.14544668X-RAY DIFFRACTION99.78
2.44-2.630.1522380.14464702X-RAY DIFFRACTION99.76
2.63-2.890.18332700.15314650X-RAY DIFFRACTION99.64
2.89-3.310.17852430.14694678X-RAY DIFFRACTION99.96
3.31-4.170.1642420.13394703X-RAY DIFFRACTION99.92
4.17-48.150.19592460.15424660X-RAY DIFFRACTION99.45

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