[English] 日本語
Yorodumi
- PDB-9fyl: Lacto-N-biosidase from Treponema denticola ATCC 35405, HisTag bou... -

+
Open data


ID or keywords:

Loading...

-
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 / homology
Function and homology information


N-acetyllactosaminidase / lacto-N-biosidase / beta-N-acetylhexosaminidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Hexosaminidase D-like / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Lacto-N-biosidase/N-acetyllactosaminidase
Similarity search - Component
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more