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

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Basic information

Entry
Database: PDB / ID: 9fyn
TitleLacto-N-biosidase from Trueperella pyogenes
Componentslacto-n-biosidase GH20
KeywordsHYDROLASE / lacto-N-biosidase / GH20
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciesTrueperella pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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: lacto-n-biosidase GH20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9633
Polymers84,8451
Non-polymers1172
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elute as a monomer in gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-9 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.788, 93.628, 93.729
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 lacto-n-biosidase GH20


Mass: 84845.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated protein 294-1043 + HisTag, linker and intact thrombin cleavage site at the N-terminus of the protein (from vector).
Source: (gene. exp.) Trueperella pyogenes (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: lacto-N-biosidase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.35 Å3/Da / Density % sol: 47.61 %
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: 1.79→41.88 Å / Num. obs: 75789 / % possible obs: 99.55 % / Redundancy: 13.8 % / Biso Wilson estimate: 71.65 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.0215 / Rrim(I) all: 0.08013 / Net I/σ(I): 16.91
Reflection shellResolution: 1.79→1.85 Å / Rmerge(I) obs: 1 / Num. unique obs: 7456 / CC1/2: 0.261 / Rpim(I) all: 1 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→41.88 Å / SU ML: 0.3521 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 3778 2.64 %
Rwork0.2063 139500 -
obs0.2073 71639 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.32 Å2
Refinement stepCycle: LAST / Resolution: 1.79→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5881 0 2 304 6187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00576012
X-RAY DIFFRACTIONf_angle_d0.64128167
X-RAY DIFFRACTIONf_chiral_restr0.0468899
X-RAY DIFFRACTIONf_plane_restr0.00851064
X-RAY DIFFRACTIONf_dihedral_angle_d5.5615815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.810.44651130.44334415X-RAY DIFFRACTION83.54
1.81-1.840.41091430.44074606X-RAY DIFFRACTION88.07
1.84-1.860.42471150.41924916X-RAY DIFFRACTION94.57
1.86-1.890.40431210.41145184X-RAY DIFFRACTION97.25
1.89-1.920.43041240.38455151X-RAY DIFFRACTION99.02
1.92-1.950.42371520.36595220X-RAY DIFFRACTION99.65
1.95-1.980.40511260.34925278X-RAY DIFFRACTION99.63
1.98-2.010.35491440.32445193X-RAY DIFFRACTION99.78
2.01-2.050.3941380.30815168X-RAY DIFFRACTION99.87
2.05-2.090.3261380.30295264X-RAY DIFFRACTION99.89
2.09-2.130.33381550.28875310X-RAY DIFFRACTION99.89
2.13-2.180.33751150.28795251X-RAY DIFFRACTION99.87
2.18-2.230.30371520.26735226X-RAY DIFFRACTION99.96
2.23-2.280.35341580.25145255X-RAY DIFFRACTION99.96
2.28-2.350.32141360.23815192X-RAY DIFFRACTION99.87
2.35-2.410.2241480.23215252X-RAY DIFFRACTION99.91
2.41-2.490.28121260.2345201X-RAY DIFFRACTION99.81
2.49-2.580.26231720.22485213X-RAY DIFFRACTION100
2.58-2.680.25111310.23285324X-RAY DIFFRACTION99.96
2.68-2.810.27341190.23815214X-RAY DIFFRACTION99.91
2.81-2.950.31081580.22155235X-RAY DIFFRACTION99.94
2.96-3.140.31171500.21685232X-RAY DIFFRACTION100
3.14-3.380.29471400.20465219X-RAY DIFFRACTION100
3.38-3.720.19491600.19165287X-RAY DIFFRACTION100
3.72-4.260.19071440.16395240X-RAY DIFFRACTION99.98
4.26-5.370.15561480.14195232X-RAY DIFFRACTION100
5.37-41.880.21011520.16495222X-RAY DIFFRACTION99.85
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)
12.08884700371-0.0467850763852-1.351359745731.24075765150.2482166834692.02812927679-0.0317146072630.22022927276-0.2040117909880.0680152283988-0.1629653655490.411474024350.150576836067-0.4949507994820.1822411148440.405115405541-0.07486478401470.009094065469680.446854410828-0.1121083127320.354841204858-0.541199159355-54.92380298061.27140034803
21.76587579717-0.328133874593-0.9205155049351.701579610140.4057243357511.874734997990.3245209325420.1601096183910.274988577771-0.0703088138189-0.2431967653490.364438161002-0.316160673111-0.385281743324-0.05831199770470.4501324745170.0601099995670.07994868103250.396510885079-0.05819389628020.3537238240220.459916923597-36.64540013385.57053486998
31.03464701875-0.247862998316-0.6897188006622.11696926722-0.2001202281343.25230037834-0.004848251729480.02214527114260.0860818964649-0.199678688920.0887455471179-0.3269757459030.1535394732312.14597719237-0.1045522362940.7459409015630.006012126003570.1503910516621.434316844720.08801903014010.6118867833981.995912018312.783315592231.8945601614
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 624 )285 - 6241 - 340
22chain 'A' and (resid 625 through 931 )625 - 931341 - 647
33chain 'A' and (resid 932 through 1043 )932 - 1043648 - 759

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