[English] 日本語
Yorodumi
- PDB-8jjt: Structure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jjt
TitleStructure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms resolution
ComponentsTIGR04348 family glycosyltransferase
KeywordsTRANSFERASE / UDP-GlcNAc
Function / homologyPutative glycosyltransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / TIGR04348 family glycosyltransferase
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWei, H. / Feng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Substrate binding and catalytic mechanism of the Se-glycosyltransferase SenB in the biosynthesis of selenoneine.
Authors: Huang, W. / Song, J. / Sun, T. / He, Y. / Li, X. / Deng, Z. / Long, F.
History
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Aug 20, 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
C: TIGR04348 family glycosyltransferase
A: TIGR04348 family glycosyltransferase
B: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7986
Polymers105,9763
Non-polymers1,8223
Water14,592810
1
C: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-5 kcal/mol
Surface area13290 Å2
MethodPISA
2
A: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-5 kcal/mol
Surface area13030 Å2
MethodPISA
3
B: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-5 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.223, 56.375, 108.445
Angle α, β, γ (deg.)90.000, 91.106, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TIGR04348 family glycosyltransferase


Mass: 35325.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: JF629_18585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A952K6X5
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 291.153 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 20000, 0.1M Hepes/NaOH pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.8929
pseudo-merohedral22-L, K, H20.1071
ReflectionResolution: 1.88→48.85 Å / Num. obs: 106627 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 15.2
Reflection shellResolution: 1.88→1.91 Å / Num. unique obs: 5198 / CC1/2: 0.771

-
Processing

Software
NameVersionClassification
Blu-Ice5.8.0267data collection
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→48.848 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.626 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.025
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2149 4962 4.655 %
Rwork0.1865 101626 -
all0.188 --
obs-106588 94.183 %
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: 27.259 Å2
Baniso -1Baniso -2Baniso -3
1-3.959 Å20 Å26.614 Å2
2---11.483 Å2-0 Å2
3---7.524 Å2
Refinement stepCycle: LAST / Resolution: 1.88→48.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7223 0 117 810 8150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137488
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177180
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.63710205
X-RAY DIFFRACTIONr_angle_other_deg1.4181.57616399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1835957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25319.806413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1331585
X-RAY DIFFRACTIONr_chiral_restr0.0890.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021783
X-RAY DIFFRACTIONr_nbd_refined0.2070.21570
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.26706
X-RAY DIFFRACTIONr_nbtor_refined0.1550.23495
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.23910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2624
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1750.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.214
X-RAY DIFFRACTIONr_nbd_other0.1380.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.215
X-RAY DIFFRACTIONr_mcbond_it2.6662.6753846
X-RAY DIFFRACTIONr_mcbond_other2.6662.6753845
X-RAY DIFFRACTIONr_mcangle_it3.4843.9994797
X-RAY DIFFRACTIONr_mcangle_other3.4843.9994798
X-RAY DIFFRACTIONr_scbond_it3.3162.9593642
X-RAY DIFFRACTIONr_scbond_other3.3152.9583643
X-RAY DIFFRACTIONr_scangle_it4.6984.3235408
X-RAY DIFFRACTIONr_scangle_other4.6974.3235409
X-RAY DIFFRACTIONr_lrange_it6.47933.5688379
X-RAY DIFFRACTIONr_lrange_other6.34532.9348181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.8920.3111000.2351900X-RAY DIFFRACTION24.0414
1.892-1.9440.3094240.2787793X-RAY DIFFRACTION101.3319
1.944-20.2833380.2077473X-RAY DIFFRACTION98.8234
2-2.0620.2632610.2027298X-RAY DIFFRACTION99.5916
2.062-2.1290.2463430.1997060X-RAY DIFFRACTION99.3691
2.129-2.2040.2192680.1936908X-RAY DIFFRACTION99.6113
2.204-2.2870.263480.2166548X-RAY DIFFRACTION99.5381
2.287-2.3810.2452940.1876412X-RAY DIFFRACTION100.4945
2.381-2.4860.2083140.1816089X-RAY DIFFRACTION99.2867
2.486-2.6080.2183220.195789X-RAY DIFFRACTION99.4305
2.608-2.7490.2163100.185511X-RAY DIFFRACTION100.1204
2.749-2.9150.1912420.1815296X-RAY DIFFRACTION99.8558
2.915-3.1160.2382140.1894990X-RAY DIFFRACTION99.7317
3.116-3.3660.212200.1924599X-RAY DIFFRACTION99.7516
3.366-3.6870.2272360.1884218X-RAY DIFFRACTION99.1982
3.687-4.1210.1712060.1663865X-RAY DIFFRACTION100.3204
4.121-4.7580.1611880.153404X-RAY DIFFRACTION99.667
4.758-5.8240.1961690.1712893X-RAY DIFFRACTION99.8695
5.824-8.2250.221150.1912301X-RAY DIFFRACTION100.7927
8.225-48.840.184500.1831279X-RAY DIFFRACTION96.6545

+
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