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- PDB-8j31: Glucosyl transferase crystallized in the presence of beta carotene -

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Basic information

Entry
Database: PDB / ID: 8j31
TitleGlucosyl transferase crystallized in the presence of beta carotene
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glucosyl transferase
Function / homologyUDP-glycosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding / Glycosyltransferase
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.78 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technology Saudi Arabia
CitationJournal: Nat Commun / Year: 2025
Title: beta-Carotene alleviates substrate inhibition caused by asymmetric cooperativity.
Authors: Liao, J. / Shahul Hameed, U.F. / Hoffmann, T.D. / Kurze, E. / Sun, G. / Steinchen, W. / Nicoli, A. / Di Pizio, A. / Kuttler, C. / Song, C. / Catici, D.A.M. / Assaad-Gerbert, F. / Hoffmann, T. ...Authors: Liao, J. / Shahul Hameed, U.F. / Hoffmann, T.D. / Kurze, E. / Sun, G. / Steinchen, W. / Nicoli, A. / Di Pizio, A. / Kuttler, C. / Song, C. / Catici, D.A.M. / Assaad-Gerbert, F. / Hoffmann, T. / Arold, S.T. / Schwab, W.G.
History
DepositionApr 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)53,7041
Polymers53,7041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.297, 155.297, 128.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Glycosyltransferase


Mass: 53703.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8K1ZRH3
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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.0, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.78→49.51 Å / Num. obs: 8122 / % possible obs: 99.6 % / Redundancy: 17.4 % / CC1/2: 0.89 / Net I/σ(I): 3.6
Reflection shellResolution: 3.78→4.23 Å / Num. unique obs: 2240 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
REFMACrefmac5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.78→49.16 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.832 / SU B: 215.549 / SU ML: 1.22 / Cross valid method: THROUGHOUT / ESU R Free: 1.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.38524 821 10.3 %RANDOM
Rwork0.36279 ---
obs0.3651 7162 97.85 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 167.007 Å2
Baniso -1Baniso -2Baniso -3
1--6.54 Å20 Å2-0 Å2
2---6.54 Å20 Å2
3---13.09 Å2
Refinement stepCycle: LAST / Resolution: 3.78→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 0 0 3566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0173636
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163479
X-RAY DIFFRACTIONr_angle_refined_deg0.9541.8444931
X-RAY DIFFRACTIONr_angle_other_deg0.3471.5618127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865.204466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77310677
X-RAY DIFFRACTIONr_chiral_restr0.0460.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02650
LS refinement shellResolution: 3.78→3.877 Å
RfactorNum. reflection% reflection
Rfree0.569 53 -
Rwork0.58 472 -
obs--91.62 %
Refinement TLS params.Method: refined / Origin x: -8.273 Å / Origin y: 40.206 Å / Origin z: -20.234 Å
111213212223313233
T1.8247 Å2-0.0859 Å2-0.0924 Å2-1.7745 Å20.07 Å2--0.7063 Å2
L2.2903 °2-1.7294 °20.3692 °2-2.5792 °2-0.5913 °2--0.4761 °2
S-0.2253 Å °-0.0459 Å °0.5723 Å °0.1164 Å °0.0777 Å °0.0135 Å °-0.0702 Å °0.0197 Å °0.1476 Å °

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