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- PDB-10zg: Novobiocin Glycosyltransferase (Ngt-1) -

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Basic information

Entry
Database: PDB / ID: 10zg
TitleNovobiocin Glycosyltransferase (Ngt-1)
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / Inactivating enzyme
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity
Similarity search - Function
: / UDP-glycosyltransferase, MGT-like / Erythromycin biosynthesis protein CIII-like, central / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
NOVOBIOCIN / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAbbas, A. / Wright, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT183745 Canada
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Ngt-1: A glycosyltransferase that confers resistance to three distinct antibiotic classes.
Authors: Abbas, A. / Sychantha, D. / Koteva, K. / Chiao, M. / Sokaribo, A. / Hackenberger, D. / Andres, S. / Wright, G.D.
History
DepositionFeb 12, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5915
Polymers45,3491
Non-polymers2,2424
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.029, 95.219, 102.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl transferase


Mass: 45348.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: BK741_28350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9X6LBE8
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside


Mass: 612.624 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H36N2O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.16 mM Magnesium acetate, 0.08 mM Na-cacodylate pH 6.7, 16% PEG 8000 (w/v) and 10% glycerol (v/v)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→27.01 Å / Num. obs: 36540 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.028 / Rrim(I) all: 0.062 / Net I/σ(I): 21
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3573 / CC1/2: 0.94 / Rpim(I) all: 0.138 / Rrim(I) all: 0.316

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.01 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 17.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 1946 5.55 %
Rwork0.1739 --
obs0.1756 35055 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→27.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 157 215 3336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093190
X-RAY DIFFRACTIONf_angle_d0.9094336
X-RAY DIFFRACTIONf_dihedral_angle_d25.7931249
X-RAY DIFFRACTIONf_chiral_restr0.055477
X-RAY DIFFRACTIONf_plane_restr0.015541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.23191340.18532206X-RAY DIFFRACTION92
2.05-2.110.20761350.16252309X-RAY DIFFRACTION95
2.11-2.170.19941410.15692307X-RAY DIFFRACTION95
2.17-2.240.19751210.15472338X-RAY DIFFRACTION95
2.24-2.320.20281460.15692263X-RAY DIFFRACTION94
2.32-2.410.20541330.16632328X-RAY DIFFRACTION95
2.41-2.520.19831400.1712336X-RAY DIFFRACTION96
2.52-2.650.20951320.17972349X-RAY DIFFRACTION96
2.65-2.820.20251440.18452368X-RAY DIFFRACTION96
2.82-3.040.23721350.19792371X-RAY DIFFRACTION96
3.04-3.340.24631410.19352434X-RAY DIFFRACTION98
3.34-3.820.19631510.17572462X-RAY DIFFRACTION99
3.82-4.810.17311400.15122470X-RAY DIFFRACTION98
4.81-27.010.20291530.18282568X-RAY DIFFRACTION97

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