[English] 日本語
Yorodumi
- PDB-9eu1: GH29A alpha-L-fucosidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9eu1
TitleGH29A alpha-L-fucosidase
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / GH29A / GH29 / fucosidase / Tris
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYang, Y.Y. / Zeuner, B. / Morth, J.P.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Independent Research Fund Denmark - Technology and Production Sciences1134-00002B Denmark
Other government202108320321
CitationJournal: Febs J. / Year: 2025
Title: Structural elucidation and characterization of GH29A alpha-l-fucosidases and the effect of pH on their transglycosylation.
Authors: Yang, Y. / Holck, J. / Thorhallsson, A.T. / Hunt, C.J. / Yang, H. / Morth, J.P. / Meyer, A.S. / Zeuner, B.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7449
Polymers97,0662
Non-polymers6787
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.167, 139.167, 110.233
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Alpha-L-fucosidase


Mass: 48532.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: F3B44_16755, FSA08_23345, O1420_06320, O1437_02900 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D1JSC1

-
Non-polymers , 6 types, 481 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium sulphate 0.1M Bis-tris pH 7.5 2.2M Ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.92→40.67 Å / Num. obs: 93816 / % possible obs: 99.77 % / Redundancy: 20.8 % / Biso Wilson estimate: 40.79 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1127 / Rpim(I) all: 0.02543 / Rrim(I) all: 0.1156 / Net I/σ(I): 17.43
Reflection shellResolution: 1.92→1.989 Å / Redundancy: 21 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 9287 / CC1/2: 0.617 / CC star: 0.873 / Rpim(I) all: 0.5004 / Rrim(I) all: 1 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→40.67 Å / SU ML: 0.2037 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.2656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 2009 2.14 %
Rwork0.1832 91795 -
obs0.1839 93804 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.96 Å2
Refinement stepCycle: LAST / Resolution: 1.92→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6670 0 39 474 7183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01086903
X-RAY DIFFRACTIONf_angle_d1.02479370
X-RAY DIFFRACTIONf_chiral_restr0.0613969
X-RAY DIFFRACTIONf_plane_restr0.0131202
X-RAY DIFFRACTIONf_dihedral_angle_d6.9692910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.26941420.26356505X-RAY DIFFRACTION99.49
1.97-2.020.29341420.24696478X-RAY DIFFRACTION99.76
2.02-2.080.25851410.24796497X-RAY DIFFRACTION99.45
2.08-2.150.26211430.2146466X-RAY DIFFRACTION99.62
2.15-2.220.24771400.20476519X-RAY DIFFRACTION99.76
2.22-2.310.21531420.19076502X-RAY DIFFRACTION99.82
2.31-2.420.2351440.19696511X-RAY DIFFRACTION99.91
2.42-2.550.23131370.19996550X-RAY DIFFRACTION99.94
2.55-2.710.24331450.22196551X-RAY DIFFRACTION99.97
2.71-2.910.22811410.19946593X-RAY DIFFRACTION99.97
2.91-3.210.26671450.22636558X-RAY DIFFRACTION100
3.21-3.670.19431440.17396618X-RAY DIFFRACTION99.99
3.67-4.630.17351490.14396621X-RAY DIFFRACTION99.62
4.63-40.670.19761540.16356826X-RAY DIFFRACTION99.74
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)
10.769022934062-0.124477109956-0.1771563269570.137210536431-0.2011851847050.4880078839570.03657692706660.3191479090280.529379209601-0.07790845884140.04923215605160.211230595161-0.258991552565-0.461759496140.0003147922928810.4351837294610.0105566785294-0.05800264798390.6411345553360.1470036131530.53940551496438.22329221818.4822501802-12.1113497413
21.64017538115-0.4699971747090.07378294203750.74063810709-0.1828183396510.532188968546-0.1663842907460.4504911163990.111955692936-0.09082938852880.088573096108-0.06459658765360.0471691963673-0.0242697781978-3.18389621948E-50.404756462024-0.0576687916421-0.05407279116880.4760437634980.008030092842040.32389055220861.5483352112.87319828485-11.5002389042
30.587450580421-0.19161656869-0.1650241858820.499847070470.2196019828740.194148470712-0.09064292707990.2563881275650.7165171849760.2293920698160.0288279320578-0.29844148995-0.1587775816130.2047635741460.0001837253465530.476261257923-0.0425556236067-0.1336674762980.5114576622820.1132994854790.59647245875767.712578522418.9184890486-8.41127471429
41.83977162039-0.339757261668-0.3537329647361.073411838870.4093564721560.592379635538-0.1123130617340.06622236341780.2936001353670.1463710019220.1176212086690.01989758934980.00398341205729-0.1664352784522.74167718254E-50.483638179495-0.00351829584063-0.1033106348280.5041060186280.08962624863080.54487517109652.196891444517.6991037956-6.49782438531
50.07271785824330.0415601372234-0.04534970377320.1469284266570.02699563447590.194305023989-0.339591568873-1.008023475090.1942588856881.291450062240.492612692127-0.204952172026-0.337776366859-0.262477547383-0.0008967788645020.7724177987780.10101769799-0.1114583685870.7590066479250.03892650508070.62251884318745.132503191711.46121091164.29099562044
61.290961512460.145756362114-1.027856115950.4810696768520.1442164602470.951255360588-0.274853148744-0.0284771847978-0.202582312494-0.01904365260910.174717828394-0.01843412220620.1712244528720.0706089989118-0.000318014029380.426181581554-0.0247367757571-0.0190543374840.430497353857-0.03000806326440.37752440403247.2979087155-5.82884941255-0.902392516695
70.7863040338360.19311481048-0.03558266271230.6473401430420.4137531197910.843282606583-0.004516380398350.2373052818720.0739657190073-0.0295643616708-0.04300959811040.280305856756-0.278598223478-0.302124730245-2.3721558704E-50.3870944567380.00461947600627-0.04709074795610.4625223662180.02493255457360.4771617760625.88840903242.247407262556.16083513146
80.6267272381320.249461764478-0.05894795619730.2766766073290.130092406520.711409801524-0.133914544034-0.00916013901117-0.2859979543640.00539342566385-0.06579009478390.4008949083520.145141711298-0.537793941849-0.0002305778497350.425746424864-0.0335253839353-0.03964120257590.532627603751-0.04826065996910.60152515579120.2025724175-4.400582662287.15387031184
91.299224883750.301842685625-0.1205031985381.879661392820.07210184384580.7580187024010.0499089409982-0.0608843648949-0.254030200195-0.00610153843292-0.136709043848-0.4407619910030.08964179555270.1169768670510.0001116838832120.3541387173980.0536473666311-0.02035870756310.4216458975930.1155663870870.44167557849447.168107375336.0505459737-34.5487557374
100.3960407263440.4599010198620.3534400441121.299413990540.2278789733540.355643395005-0.1982083987441.302921486010.569577124042-1.305353627170.09481142254341.23784629685-1.00546657634-0.959637795924-0.02639644857791.074847134360.168894396611-0.06162730498091.059353170330.1769458449270.89498332115535.40763540429.7142891022-49.4383748462
111.783623088521.073262219280.5999378262551.395475744730.7221820378061.57762175624-0.0938583792484-0.0826989416666-0.185547454239-0.0252527658079-0.03272202847550.06337083916270.109860452211-0.0381700516542-0.0001997069797450.3692587737720.0452623831570.06311211947040.374977656960.02607174845920.38400723306820.291721744423.7787626929-40.6057194747
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 40 )AA21 - 401 - 20
22chain 'A' and (resid 41 through 162 )AA41 - 16221 - 142
33chain 'A' and (resid 163 through 193 )AA163 - 193143 - 173
44chain 'A' and (resid 194 through 260 )AA194 - 260174 - 240
55chain 'A' and (resid 261 through 281 )AA261 - 281241 - 261
66chain 'A' and (resid 282 through 348 )AA282 - 348262 - 328
77chain 'A' and (resid 349 through 394 )AA349 - 394329 - 374
88chain 'A' and (resid 395 through 434 )AA395 - 434375 - 414
99chain 'B' and (resid 23 through 250 )BC23 - 2501 - 228
1010chain 'B' and (resid 251 through 269 )BC251 - 269229 - 247
1111chain 'B' and (resid 270 through 434 )BC270 - 434248 - 412

+
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