[English] 日本語
Yorodumi
- PDB-8jjn: Structure of SenB in complex with UDP-Glc and PO4- at 1.98 Angstr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jjn
TitleStructure of SenB in complex with UDP-Glc and PO4- at 1.98 Angstroms resolution
ComponentsTIGR04348 family glycosyltransferase
KeywordsTRANSFERASE / Complex with UDP-Glc and PO4-
Function / homologyPutative glycosyltransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / TIGR04348 family glycosyltransferase
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHuang, W. / Long, F.
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 1.1Nov 13, 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)107,0869
Polymers105,1023
Non-polymers1,9846
Water7,800433
1
C: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6953
Polymers35,0341
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-5 kcal/mol
Surface area13490 Å2
MethodPISA
2
A: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6953
Polymers35,0341
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-13 kcal/mol
Surface area12780 Å2
MethodPISA
3
B: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6953
Polymers35,0341
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-5 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.825, 55.792, 108.076
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein TIGR04348 family glycosyltransferase


Mass: 35033.938 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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 291.153 K / Method: vapor diffusion, sitting drop
Details: 20%PEG8000, 0.2M(NH4SO4, 0.1M Hepes pH 7.5,10% 2-propanol

-
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: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.98→49.57 Å / Num. obs: 89982 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.22 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 1.98→2.01 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 575 / CC1/2: 0.58

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Blu-Icedata collection
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→48.55 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 4529 5.03 %
Rwork0.191 --
obs0.1925 89952 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7221 0 108 433 7762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087471
X-RAY DIFFRACTIONf_angle_d0.97710180
X-RAY DIFFRACTIONf_dihedral_angle_d8.1781132
X-RAY DIFFRACTIONf_chiral_restr0.0531162
X-RAY DIFFRACTIONf_plane_restr0.0111336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-20.3281340.27392835X-RAY DIFFRACTION100
2-2.030.30691600.2632800X-RAY DIFFRACTION100
2.03-2.050.28021590.2492829X-RAY DIFFRACTION100
2.05-2.080.30911140.23392867X-RAY DIFFRACTION100
2.08-2.10.26831590.23272809X-RAY DIFFRACTION100
2.1-2.130.27341670.21632831X-RAY DIFFRACTION100
2.13-2.160.27741610.2142820X-RAY DIFFRACTION100
2.16-2.20.23491550.20382771X-RAY DIFFRACTION100
2.2-2.230.2551670.19912858X-RAY DIFFRACTION100
2.23-2.270.23681550.20472801X-RAY DIFFRACTION100
2.27-2.310.23571480.19942857X-RAY DIFFRACTION100
2.31-2.350.2721230.19282873X-RAY DIFFRACTION100
2.35-2.390.24161610.19062796X-RAY DIFFRACTION100
2.39-2.440.22541450.19682859X-RAY DIFFRACTION100
2.44-2.490.25311560.19092806X-RAY DIFFRACTION100
2.49-2.550.20711420.18432862X-RAY DIFFRACTION100
2.55-2.620.26451690.18552808X-RAY DIFFRACTION100
2.62-2.690.19871380.18012876X-RAY DIFFRACTION100
2.69-2.770.22041190.18222891X-RAY DIFFRACTION100
2.77-2.860.18831580.18732793X-RAY DIFFRACTION100
2.86-2.960.25421940.19042833X-RAY DIFFRACTION100
2.96-3.080.22611320.19822879X-RAY DIFFRACTION100
3.08-3.220.24121490.19322849X-RAY DIFFRACTION100
3.22-3.390.21761420.19422862X-RAY DIFFRACTION100
3.39-3.60.19651480.18782873X-RAY DIFFRACTION100
3.6-3.870.19291170.17342889X-RAY DIFFRACTION100
3.88-4.260.21790.16792848X-RAY DIFFRACTION100
4.26-4.880.17121470.16232903X-RAY DIFFRACTION100
4.88-6.150.21051800.20182867X-RAY DIFFRACTION100
6.15-48.550.18861510.19152978X-RAY DIFFRACTION99

+
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