[English] 日本語
Yorodumi
- PDB-8x3u: tll1591 with alpha_glucan 3sugar -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x3u
Titletll1591 with alpha_glucan 3sugar
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / tll1591 with alpha_glucan 3sugar
Function / homology
Function and homology information


biosynthetic process / glycosyltransferase activity / nucleotide binding
Similarity search - Function
Glycosyl transferase 4-like domain / : / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glycosyl transferase
Similarity search - Component
Biological speciesThermosynechococcus vestitus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsSu, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171255 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Glucosyltransferase TeGSS from Thermosynechococcus elongatus produces an alpha-1,2-glucan.
Authors: Qu, X. / An, Q. / Sayed, H. / Cui, L. / Mayo, K.H. / Su, J.Y.
History
DepositionNov 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
B: Glycosyl transferase
A: Glycosyl transferase
C: Glycosyl transferase
D: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,26612
Polymers161,6324
Non-polymers3,6348
Water3,981221
1
B: Glycosyl transferase
hetero molecules

D: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6336
Polymers80,8162
Non-polymers1,8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/61
Buried area5880 Å2
ΔGint-9 kcal/mol
Surface area26160 Å2
MethodPISA
2
A: Glycosyl transferase
hetero molecules

C: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6336
Polymers80,8162
Non-polymers1,8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_544x-y,x-1,z-1/61
Buried area5800 Å2
ΔGint-10 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.135, 156.135, 187.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein
Glycosyl transferase


Mass: 40407.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1) (bacteria)
Gene: tll1591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DIJ4
#2: Polysaccharide
alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-2DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2-2/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(2+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.58→20 Å / Num. obs: 80733 / % possible obs: 99.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 18
Reflection shellResolution: 2.58→2.63 Å / Rmerge(I) obs: 1.02 / Num. unique obs: 4647

-
Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→20 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3039 2005 2.48 %
Rwork0.277 --
obs0.2777 80725 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10844 0 236 221 11301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411384
X-RAY DIFFRACTIONf_angle_d0.84815556
X-RAY DIFFRACTIONf_dihedral_angle_d21.3171520
X-RAY DIFFRACTIONf_chiral_restr0.0471756
X-RAY DIFFRACTIONf_plane_restr0.0051984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.640.37321440.34375659X-RAY DIFFRACTION100
2.64-2.720.40071420.33965621X-RAY DIFFRACTION100
2.72-2.80.3661450.32835632X-RAY DIFFRACTION100
2.8-2.890.371400.31815641X-RAY DIFFRACTION100
2.89-2.990.38491410.3125603X-RAY DIFFRACTION100
2.99-3.110.33531460.31185625X-RAY DIFFRACTION100
3.11-3.250.30711430.29375617X-RAY DIFFRACTION100
3.25-3.420.34231430.29835609X-RAY DIFFRACTION100
3.42-3.630.33681470.27375643X-RAY DIFFRACTION100
3.63-3.910.29691370.27035630X-RAY DIFFRACTION99
3.91-4.30.27061410.25915599X-RAY DIFFRACTION99
4.3-4.910.25661450.24955638X-RAY DIFFRACTION99
4.91-6.160.27691430.27195608X-RAY DIFFRACTION99
6.16-200.27741480.2515595X-RAY DIFFRACTION98

+
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