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- PDB-9jn3: Crystal structure of AvpGT in complex with Ara-A -

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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 / glycosyltransferase activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Comment: antivirus*YM
#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

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Experimental details

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Experiment

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

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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

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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

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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

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