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- PDB-9jma: Crystal structure of glycosyltransferase AvpGT -

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Basic information

Entry
Database: PDB / ID: 9jma
TitleCrystal structure of glycosyltransferase AvpGT
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 / URIDINE-5'-DIPHOSPHATE / 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: 2.2 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 20, 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)68,9156
Polymers68,0582
Non-polymers8574
Water6,990388
1
A: GalNAc(5)-diNAcBac-PP-undecaprenol beta-1,3-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4583
Polymers34,0291
Non-polymers4282
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)34,4583
Polymers34,0291
Non-polymers4282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.362, 95.144, 70.484
Angle α, β, γ (deg.)90.00, 97.16, 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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
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: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→42.09 Å / Num. obs: 32146 / % possible obs: 99.74 % / Redundancy: 6.5 % / CC1/2: 0.955 / Net I/σ(I): 5.07
Reflection shellResolution: 2.2→2.279 Å / Mean I/σ(I) obs: 3.01 / Num. unique obs: 3202 / CC1/2: 0.823

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.09 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 1594 4.96 %
Rwork0.195 --
obs0.1976 32146 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 52 391 5243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084966
X-RAY DIFFRACTIONf_angle_d0.916790
X-RAY DIFFRACTIONf_dihedral_angle_d7.653700
X-RAY DIFFRACTIONf_chiral_restr0.052766
X-RAY DIFFRACTIONf_plane_restr0.01896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.35311550.26252759X-RAY DIFFRACTION100
2.27-2.350.27261460.23622732X-RAY DIFFRACTION100
2.35-2.450.33961520.22082764X-RAY DIFFRACTION100
2.45-2.560.30311390.22232781X-RAY DIFFRACTION100
2.56-2.690.33771280.21022788X-RAY DIFFRACTION100
2.69-2.860.26351510.20112763X-RAY DIFFRACTION100
2.86-3.080.21661450.18642762X-RAY DIFFRACTION100
3.08-3.390.22571490.182789X-RAY DIFFRACTION100
3.39-3.880.22591500.18282765X-RAY DIFFRACTION100
3.88-4.890.20631460.16662805X-RAY DIFFRACTION100
4.89-42.090.18671330.18472844X-RAY DIFFRACTION100

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