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- PDB-9fyl: Lacto-N-biosidase from Treponema denticola ATCC 35405, HisTag bou... -

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Basic information

Entry
Database: PDB / ID: 9fyl
TitleLacto-N-biosidase from Treponema denticola ATCC 35405, HisTag bound in active site
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 / 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: 2.24 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: Glycoside hydrolase family 20 catalytic domain-containing protein
B: Glycoside hydrolase family 20 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0764
Polymers75,9452
Non-polymers1312
Water59433
1
A: Glycoside hydrolase family 20 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0382
Polymers37,9721
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 20 catalytic domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0382
Polymers37,9721
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.917, 89.471, 93.757
Angle α, β, γ (deg.)90.000, 127.000, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 38 through 64 or resid 67...
d_2ens_1(chain "B" and (resid 38 through 64 or resid 67...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSGLNGLNAA38 - 645 - 31
d_12GLYGLYASNASNAA67 - 8934 - 56
d_13TYRTYRASNASNAA91 - 21558 - 182
d_14LEULEUTYRTYRAA217 - 246184 - 213
d_15GLYGLYILEILEAA248 - 302215 - 269
d_16ALAALAASNASNAA304 - 334271 - 301
d_17ASNASNSERSERAA336 - 338303 - 305
d_18TYRTYRHISHISAA340 - 362307 - 329
d_21LYSLYSGLNGLNBB38 - 645 - 31
d_22GLYGLYASNASNBB67 - 8934 - 56
d_23TYRTYRASNASNBB91 - 21558 - 182
d_24LEULEUTYRTYRBB217 - 246184 - 213
d_25GLYGLYILEILEBB248 - 302215 - 269
d_26ALAALAASNASNBB304 - 334271 - 301
d_27ASNASNSERSERBB336 - 338303 - 305
d_28TYRTYRHISHISBB340 - 362307 - 329

NCS oper: (Code: givenMatrix: (-0.272046913077, -0.0296320066868, -0.961827646341), (0.0179980201791, -0.999507612231, 0.0257022248341), (-0.96211566267, -0.0103187824623, 0.272446277959)Vector: 12. ...NCS oper: (Code: given
Matrix: (-0.272046913077, -0.0296320066868, -0.961827646341), (0.0179980201791, -0.999507612231, 0.0257022248341), (-0.96211566267, -0.0103187824623, 0.272446277959)
Vector: 12.6759875083, 31.0065704957, 67.9098649322)

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Components

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


Mass: 37972.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Peptide signal has been removed and linker "LE" and 6xHis-Tag has been added at the C-terminus of the protein
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Gene: TDE_1723 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73LY9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.84 Å3/Da / Density % sol: 56.74 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.24→46.31 Å / Num. obs: 40862 / % possible obs: 99.79 % / Redundancy: 6.8 % / Biso Wilson estimate: 71.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07793 / Rrim(I) all: 0.08431 / Net I/σ(I): 9.6
Reflection shellResolution: 2.24→2.32 Å / Rmerge(I) obs: 1 / Num. unique obs: 4044 / CC1/2: 0.323 / 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: 2.24→46.31 Å / SU ML: 0.4749 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.6937
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2689 1990 4.88 %
Rwork0.2319 38749 -
obs0.2338 40739 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.99 Å2
Refinement stepCycle: LAST / Resolution: 2.24→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 2 33 5309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01485408
X-RAY DIFFRACTIONf_angle_d1.45027318
X-RAY DIFFRACTIONf_chiral_restr0.117782
X-RAY DIFFRACTIONf_plane_restr0.0147934
X-RAY DIFFRACTIONf_dihedral_angle_d8.9956714
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.791446732607 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30.56161390.48952704X-RAY DIFFRACTION97.93
2.3-2.360.47171410.45242740X-RAY DIFFRACTION99.14
2.36-2.430.44981380.41142734X-RAY DIFFRACTION99.51
2.43-2.510.39041430.35992762X-RAY DIFFRACTION99.9
2.51-2.60.37691430.36822782X-RAY DIFFRACTION99.93
2.6-2.70.42631430.37832765X-RAY DIFFRACTION99.79
2.7-2.820.40551410.33252757X-RAY DIFFRACTION99.97
2.82-2.970.35991420.29092750X-RAY DIFFRACTION99.93
2.97-3.160.34131420.28162795X-RAY DIFFRACTION99.97
3.16-3.40.30361430.30072757X-RAY DIFFRACTION99.83
3.4-3.750.27921430.22782788X-RAY DIFFRACTION99.69
3.75-4.290.23661420.2062776X-RAY DIFFRACTION99.97
4.29-5.40.20721450.18432795X-RAY DIFFRACTION99.93
5.4-46.310.22141450.1772844X-RAY DIFFRACTION99.53
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)
10.584252906717-0.162097152568-0.5166126562471.348273498880.5390566533173.03094180048-0.0266643306924-0.456627782051.026735682660.0793189130878-0.003869916442190.131517223534-1.426666325350.08580075302270.001402914776031.231637750170.112332887355-0.01025449611340.874757332545-0.09882023583581.1056380005238.473256714416.668379601514.2400089335
20.2930926755215.71237827776E-5-0.2934140537770.3628255155030.3089543682560.371812835220.2907830097870.3547823936280.524360399374-0.5167807477690.03009270826440.311254494439-0.7847304623370.08446335586960.000666972808460.788953590159-0.03320744691960.1352463689560.9469301779890.1194359825260.85776066168252.29885966666.48155674025-1.66062665142
32.98367898489-1.06893470622-0.21003513812.52142533435-0.6684562186282.28110552516-0.04454992244030.141471141346-0.273950792394-0.1196394367980.08655074463530.453995566691-0.0262577348231-0.127877658678-0.0002362294278590.580577656410.0417422553312-0.01564738866540.728967042290.02604132731760.8241010499336.7986599262-1.397184205973.32340221819
40.243679641892-0.01621688003460.631257166040.6007394525630.3406026188341.39281734642-0.576461250337-0.432711874320.666806835424-0.5360154439710.3815089871420.717401362848-1.35052793146-0.539397261834-0.02417342547470.7773665528180.1634887483030.08444686041250.9497228245320.1681508619141.215096158327.02913113213.16462938146.01730900473
50.0706456422287-0.0250660160889-0.2081322657690.4878351726470.3887139014970.2808561044560.07039901906610.233838609651-0.5183604779360.777414805907-1.165799160150.261848872676-0.6365031447070.351384037786-0.02605365512341.26680143930.2952775466240.0380284371521.314806868510.2484128927651.8329400690413.833165345515.236344422816.2347107909
62.398341222690.51881401853-0.5516493191493.76396518751-0.8068755632493.78554380737-0.127989056747-0.0311240301335-0.680997639350.2412077904060.2344446434450.3067143237150.916648834289-0.5255016164160.0008506038167291.05581821190.002550425504620.07453399702920.8825817500910.08424294201970.850394203536-8.0901828596121.454128179828.0760486571
70.324086035981-0.2911934474260.5266229706331.10453703651-0.3413899903760.6677756191590.206834063621-0.0281139757820.3319921207540.6847980838210.1709734479580.090722104087-0.729532838006-0.1571513732950.0009922423910590.6946243302660.1056094497190.06619305117010.9227167330380.07754103870360.77435633991-3.0441969863640.285751358222.7475235462
80.4336809927090.377615542229-0.5291093691212.19708035591-0.6571397666932.46346915569-0.290520060553-0.534586123775-0.02564295882471.198733367370.196476692679-0.543097900333-0.1543032220470.298062509089-0.0002111787213281.187242171450.215263157356-0.07533774503360.9907281695650.03152888949420.9216333374913.0131355348335.194269483437.9334295992
91.789820249721.24152378787-0.1964694957920.875061454728-0.1258960442630.6004697406970.119620765401-0.415272724822-0.5470801220421.146240573290.23673207284-0.3430389617510.7093763947960.251481831848-0.002278532773671.667453143690.308450077824-0.1074671616391.094536173640.0561350679270.8657114625911.7122073395922.966927240945.4073261712
100.187925878730.388102359812-0.2157259326330.424785626423-0.2653640804390.2192971137890.130335382339-0.419440681756-0.3704284851190.0730711967267-0.5572042393130.29542807453-0.5460590740280.254170452085-0.001599171747572.056986878750.3434777553280.07306750857671.308144338170.1668933981021.09630084663-7.0370419264216.336370432759.1139359856
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 38 through 115 )AA38 - 1151 - 78
22chain 'A' and (resid 116 through 148 )AA116 - 14879 - 111
33chain 'A' and (resid 149 through 315 )AA149 - 315112 - 278
44chain 'A' and (resid 316 through 340 )AA316 - 340279 - 303
55chain 'A' and (resid 341 through 362 )AA341 - 362304 - 325
66chain 'B' and (resid 38 through 194 )BE38 - 1941 - 157
77chain 'B' and (resid 195 through 221 )BE195 - 221158 - 184
88chain 'B' and (resid 222 through 289 )BE222 - 289185 - 252
99chain 'B' and (resid 290 through 340 )BE290 - 340253 - 303
1010chain 'B' and (resid 341 through 362 )BE341 - 362304 - 325

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