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- PDB-9v0l: UDP-binding PsBGluT, a tetrahydrobiopterin glucosyltransferase fr... -

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Basic information

Entry
Database: PDB / ID: 9v0l
TitleUDP-binding PsBGluT, a tetrahydrobiopterin glucosyltransferase from Pseudanabaena sp. Chao 1811
Componentstetrahydrobiopterin glucosyltransferases
KeywordsTRANSFERASE / GT-B glycosyltransferases / pterin glycosyltransferases / retaining glycosyltransferases
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesPseudanabaena sp. Chao 1811 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZang, R.J. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32430001 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structural analysis of the tetrahydrobiopterin glucosyltransferase PsBGluT from Pseudanabaena sp. Chao 1811.
Authors: Zang, R. / Jiang, Y. / Zhou, C.Z.
History
DepositionMay 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tetrahydrobiopterin glucosyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6082
Polymers40,2041
Non-polymers4041
Water3,927218
1
A: tetrahydrobiopterin glucosyltransferases
hetero molecules

A: tetrahydrobiopterin glucosyltransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2164
Polymers80,4082
Non-polymers8082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area2030 Å2
ΔGint-10 kcal/mol
Surface area28010 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-8 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.970, 176.970, 66.171
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-557-

HOH

21A-649-

HOH

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Components

#1: Protein tetrahydrobiopterin glucosyltransferases


Mass: 40203.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a GT-B glycosyltransferase, and may be a retaining glycosyltransferase.
Source: (gene. exp.) Pseudanabaena sp. Chao 1811 (bacteria) / Production host: Escherichia coli (E. coli)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.72 Å3/Da / Density % sol: 66.94 % / Description: hexagonal
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M sodium acetate pH 5.0, 2M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 6, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.3→13.04 Å / Num. obs: 27426 / % possible obs: 99.4 % / Redundancy: 13.9 % / Biso Wilson estimate: 18.553 Å2 / Rpim(I) all: 0.029 / Net I/σ(I): 24.7
Reflection shellResolution: 2.3→2.39 Å / Num. unique obs: 2848 / Rpim(I) all: 0.16

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisPro171.39.35cdata reduction
Aimless0.8.2data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→13.04 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1293 4.72 %
Rwork0.2143 --
obs0.2166 27406 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→13.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 25 218 3014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042859
X-RAY DIFFRACTIONf_angle_d0.6823890
X-RAY DIFFRACTIONf_dihedral_angle_d12.8771025
X-RAY DIFFRACTIONf_chiral_restr0.045439
X-RAY DIFFRACTIONf_plane_restr0.004495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.37481480.30822834X-RAY DIFFRACTION100
2.39-2.50.33191320.27712843X-RAY DIFFRACTION100
2.5-2.630.31771650.2582856X-RAY DIFFRACTION100
2.63-2.790.31051570.26462839X-RAY DIFFRACTION100
2.79-3.010.30551300.25462899X-RAY DIFFRACTION100
3.01-3.310.25051300.22662900X-RAY DIFFRACTION100
3.31-3.770.2911390.20012905X-RAY DIFFRACTION100
3.77-4.720.18941500.15722950X-RAY DIFFRACTION100
4.72-100.18831420.16253087X-RAY DIFFRACTION100

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