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- PDB-9fyo: Lacto-N-biosidase from Trueperella pyogenes -

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Basic information

Entry
Database: PDB / ID: 9fyo
TitleLacto-N-biosidase from Trueperella pyogenes
ComponentsTrpyGH20
KeywordsHYDROLASE / lacto-N-biosidase / GH20
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciesTrueperella pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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

Downloads & links

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Assembly

Deposited unit
A: TrpyGH20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4055
Polymers84,8451
Non-polymers5594
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.759, 93.686, 94.037
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 TrpyGH20


Mass: 84845.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated protein 294-1043 Additional AA from vector at the N-terminus of the protein (Linker, HisTag and intact thrombin cleavage site)
Source: (gene. exp.) Trueperella pyogenes (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: lacto-N-biosidase
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0,01 M Nickel II chloride hexahydrate, 0,1M Tris pH8,5 and 20% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 2.77→65.3 Å / Num. obs: 20739 / % possible obs: 98.46 % / Redundancy: 13.4 % / Biso Wilson estimate: 77.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Net I/σ(I): 20.31
Reflection shellResolution: 2.77→2.86 Å / Rmerge(I) obs: 1 / Num. unique obs: 2036 / CC1/2: 0.89 / Rpim(I) all: 0.281

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→65.3 Å / SU ML: 0.3793 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 1083 5.22 %
Rwork0.2272 19650 -
obs0.2292 20733 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.45 Å2
Refinement stepCycle: LAST / Resolution: 2.77→65.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5881 0 29 23 5933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01266038
X-RAY DIFFRACTIONf_angle_d1.62768203
X-RAY DIFFRACTIONf_chiral_restr0.0861909
X-RAY DIFFRACTIONf_plane_restr0.01221065
X-RAY DIFFRACTIONf_dihedral_angle_d7.7876831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.890.41951180.40132454X-RAY DIFFRACTION99.88
2.89-3.050.37331310.3372473X-RAY DIFFRACTION99.96
3.05-3.240.31661410.3072432X-RAY DIFFRACTION99.92
3.24-3.490.34871330.30582471X-RAY DIFFRACTION99.92
3.49-3.840.26611730.25442278X-RAY DIFFRACTION94.09
3.84-4.390.27791470.21542332X-RAY DIFFRACTION94.26
4.39-5.530.20051400.18862535X-RAY DIFFRACTION99.96
5.53-65.30.23791000.18082675X-RAY DIFFRACTION99.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.237172007351.0711135482-0.1914716998861.84883904748-0.3598085932821.90038758911-0.1111897358990.2452172080790.210208996055-0.2382625466140.1833296335640.4285685898310.0816338360041-0.4725186251350.0002402373296730.6987176944180.0315010587775-0.0805571843010.7227361477110.1132068222270.721477604201-22.474508706423.3525344026-30.7981496874
21.568444621310.666096608243-0.2788909017071.67386464196-0.1016682801361.86816015010.166286133252-0.1415308352940.03676138684770.1557352297430.06734102852230.3560511509860.0318913222049-0.4464082783230.0002326538068550.711714356494-0.02309102554670.01472677563220.7200687917680.113233607490.680769753145-22.935535001717.10449232-15.3661918801
30.2794644062180.134110462964-0.144235538690.3613619846190.00289603931550.734231251-0.195780443566-0.2551291712680.342125841896-0.36670420180.178344310181-1.79095988975-0.1104618272140.06234382739740.0003136399710711.01010203525-0.09239067853440.0275207958920.977855693548-0.2036173815241.5400741347-20.674045154521.185369760726.7294232178
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 285 through 600 )285 - 6001 - 316
22chain 'A' and (resid 601 through 931 )601 - 931317 - 647
33chain 'A' and (resid 932 through 1043 )932 - 1043648 - 759

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