[English] 日本語
Yorodumi
- PDB-9jn3: Crystal structure of AvpGT in complex with Ara-A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jn3
TitleCrystal structure of AvpGT in complex with Ara-A
ComponentsGalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase
KeywordsTRANSFERASE / glycosyltransferase
Function / homologyGalNAc5-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / hexosyltransferase activity / biosynthetic process / Nucleotide-diphospho-sugar transferases / Chem-RAB / URIDINE-5'-DIPHOSPHATE-GLUCOSE / GalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase
Function and homology information
Biological speciesStreptomyces sp. AVP053U2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, J.H. / Wang, Z.Q. / Zhang, Z.Y. / Chen, W.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371303 China
CitationJournal: Acs Catalysis / Year: 2025
Title: Efficient Synthesis of Glycodiversified Nucleoside Analogues by a Thermophilic Promiscuous Glycosyltransferase
Authors: Wang, Z. / Li, J. / Wang, X. / Jin, B. / Zhou, L. / Zhao, Z. / Gu, M. / Song, X. / Wang, J. / Deng, Z. / Wu, S. / Zhang, Z. / Chen, W.
History
DepositionSep 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase
B: GalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7748
Polymers68,0582
Non-polymers1,7166
Water2,270126
1
A: GalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8874
Polymers34,0291
Non-polymers8583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8874
Polymers34,0291
Non-polymers8583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.302, 95.114, 70.988
Angle α, β, γ (deg.)90.00, 101.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein GalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase / glycosyltransferase AvpGT


Mass: 34029.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. AVP053U2 (bacteria) / Gene: pglI, APS67_002972 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1D2IE05, GalNAc5-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RAB / 2-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 9-BETA-D-ARABINOFURANOSYL-ADENINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 6000, 0.1 M Hepes, 0.2 M Calcium chloride dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→24.81 Å / Num. obs: 22081 / % possible obs: 99.61 % / Redundancy: 6.5 % / CC1/2: 0.983 / Net I/σ(I): 6.64
Reflection shellResolution: 2.4→2.486 Å / Mean I/σ(I) obs: 2.34 / Num. unique obs: 2187 / CC1/2: 0.816

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9JMA

9jma


Resolution: 2.4→24.81 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 1094 4.96 %
Rwork0.181 --
obs0.1845 22068 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 112 127 4825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114812
X-RAY DIFFRACTIONf_angle_d1.2516593
X-RAY DIFFRACTIONf_dihedral_angle_d11.339754
X-RAY DIFFRACTIONf_chiral_restr0.065757
X-RAY DIFFRACTIONf_plane_restr0.013858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.2971370.20032618X-RAY DIFFRACTION100
2.51-2.640.34861280.2222611X-RAY DIFFRACTION100
2.64-2.810.29191380.21722614X-RAY DIFFRACTION100
2.81-3.020.30961320.20612602X-RAY DIFFRACTION100
3.02-3.330.27831240.20122658X-RAY DIFFRACTION100
3.33-3.810.24581180.17792613X-RAY DIFFRACTION100
3.81-4.790.21121660.15372617X-RAY DIFFRACTION99
4.79-24.810.21841510.16462641X-RAY DIFFRACTION100

+
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