[English] 日本語
Yorodumi
- PDB-8z48: Beta-galactosidase from Bacteroides xylanisolvens (complex with m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z48
TitleBeta-galactosidase from Bacteroides xylanisolvens (complex with methyl beta-galactopyranose)
ComponentsBeta-galactosidase
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
methyl beta-D-galactopyranoside / Beta-galactosidase
Similarity search - Component
Biological speciesBacteroides xylanisolvens XB1A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsNakajima, M. / Motouchi, S. / Kobayashi, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2025
Title: Structure and function of a beta-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium.
Authors: Nakazawa, Y. / Kageyama, M. / Matsuzawa, T. / Liang, Z. / Kobayashi, K. / Shimizu, H. / Maeda, K. / Masuhiro, M. / Motouchi, S. / Kumano, S. / Tanaka, N. / Kuramochi, K. / Nakai, H. / Taguchi, H. / Nakajima, M.
History
DepositionApr 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,1638
Polymers250,3864
Non-polymers7774
Water23,9421329
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Homotetramer according to PISA analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.765, 50.839, 229.445
Angle α, β, γ (deg.)90.000, 96.099, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Beta-galactosidase


Mass: 62596.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides xylanisolvens XB1A (bacteria)
Gene: BXY_22780 / Production host: Escherichia coli (E. coli) / References: UniProt: D6CYU7
#2: Sugar
ChemComp-MBG / methyl beta-D-galactopyranoside / METHYL-BETA-GALACTOSE / methyl beta-D-galactoside / methyl D-galactoside / methyl galactoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalp[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: potassium thiocyanate, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→45.91 Å / Num. obs: 194503 / % possible obs: 98.2 % / Redundancy: 3.1 % / CC1/2: 0.997 / Net I/σ(I): 8.1
Reflection shellResolution: 1.94→1.97 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 9674 / CC1/2: 0.768

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→45.629 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.251 9831 5.054 %
Rwork0.2113 184670 -
all0.213 --
obs-194501 98.081 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.79 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0.001 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.94→45.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16098 0 52 1329 17479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01216582
X-RAY DIFFRACTIONr_bond_other_d0.0020.01615422
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.81222510
X-RAY DIFFRACTIONr_angle_other_deg0.8411.75935578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21852010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.41564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.844102764
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.93110756
X-RAY DIFFRACTIONr_chiral_restr0.0760.22414
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219470
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023874
X-RAY DIFFRACTIONr_nbd_refined0.2060.23305
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.214327
X-RAY DIFFRACTIONr_nbtor_refined0.1830.28084
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.28231
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.21211
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1190.231
X-RAY DIFFRACTIONr_nbd_other0.2520.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.214
X-RAY DIFFRACTIONr_mcbond_it2.052.4668064
X-RAY DIFFRACTIONr_mcbond_other2.052.4668064
X-RAY DIFFRACTIONr_mcangle_it2.9544.42410066
X-RAY DIFFRACTIONr_mcangle_other2.9544.42510067
X-RAY DIFFRACTIONr_scbond_it2.772.7678518
X-RAY DIFFRACTIONr_scbond_other2.772.7678519
X-RAY DIFFRACTIONr_scangle_it4.3314.93212444
X-RAY DIFFRACTIONr_scangle_other4.3314.93212445
X-RAY DIFFRACTIONr_lrange_it5.56224.8119289
X-RAY DIFFRACTIONr_lrange_other5.52324.71419017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.94-1.990.3337020.306137150.307144960.9260.93899.4550.277
1.99-2.0450.3037210.281134760.282142570.9410.94999.57920.249
2.045-2.1040.3166600.267129980.269137210.9380.95699.54080.234
2.104-2.1680.296410.249126250.251133600.9460.96299.29640.217
2.168-2.2390.2766810.237122750.239130280.9520.96699.44730.207
2.239-2.3180.2926080.233119150.235126070.9490.96799.33370.205
2.318-2.4050.286210.22113410.223120720.9520.97299.08880.193
2.405-2.5030.2565990.211109320.213116550.9620.97498.93610.186
2.503-2.6140.2486000.201104970.203112320.9610.97798.79810.179
2.614-2.7410.2595680.20399590.206107190.960.97698.20880.184
2.741-2.8890.2565210.19895780.201102950.9630.97798.09620.183
2.889-3.0630.2624460.20490200.20696680.9610.97697.91060.192
3.063-3.2740.2474220.20384670.20590990.9630.97797.69210.195
3.274-3.5340.234090.20678170.20785380.970.97896.34570.205
3.534-3.870.2213810.19170940.19278820.9740.98194.83630.195
3.87-4.3220.2073270.17663560.17771220.9770.98393.8360.188
4.322-4.9840.1993100.16556230.16763370.9820.98693.62470.181
4.984-6.0860.2232820.19348730.19553940.9780.98295.56920.206
6.086-8.5310.2322170.20639000.20842850.9750.97996.07930.222
8.531-45.6290.2531150.2222100.22225170.9690.97492.37190.252

+
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