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- PDB-8wp5: Crystal structure of LbUGT1 in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 8wp5
TitleCrystal structure of LbUGT1 in complex with UDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Lycibarbarspermidines / Biosynthesis / Glycosyltransferase
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesLycium barbarum (goji berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57005953651 Å
AuthorsHu, D. / Wang, G.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Functional and structural dissection of glycosyltransferases underlying the glycodiversity of wolfberry-derived bioactive ingredients lycibarbarspermidines.
Authors: Li, S.Y. / Wang, G.Q. / Long, L. / Gao, J.L. / Zhou, Z.Q. / Wang, Y.H. / Lv, J.M. / Chen, G.D. / Hu, D. / Abe, I. / Gao, H.
History
DepositionOct 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
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.year / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4123
Polymers54,9731
Non-polymers4402
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-20 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.240, 122.240, 81.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

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Components

#1: Protein Glycosyltransferase


Mass: 54972.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycium barbarum (goji berry) / 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 292.2 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES sodium hydroxide, 200 mM Ammonium sulfate, 10% 2-propanol, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.57→48.902 Å / Num. obs: 20277 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 60.6546327524 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.2
Reflection shellResolution: 2.57→2.64 Å / Num. unique obs: 1468 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57005953651→48.901758191 Å / SU ML: 0.391823981736 / Cross valid method: FREE R-VALUE / σ(F): 1.34355005509 / Phase error: 31.1015916996
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285618105289 2000 9.8867961837 %
Rwork0.242887677682 18229 -
obs0.247081308695 20229 99.9802303168 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.7668723766 Å2
Refinement stepCycle: LAST / Resolution: 2.57005953651→48.901758191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 26 21 3783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002975737370663847
X-RAY DIFFRACTIONf_angle_d0.6426878123095202
X-RAY DIFFRACTIONf_chiral_restr0.0418318315667577
X-RAY DIFFRACTIONf_plane_restr0.0053735006833664
X-RAY DIFFRACTIONf_dihedral_angle_d7.3059673712290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5701-2.63430.4002965620911400.338745299911279X-RAY DIFFRACTION99.9295774648
2.6343-2.70550.4088996152121400.3032609254461271X-RAY DIFFRACTION100
2.7055-2.78520.3684715512341400.3128862382721279X-RAY DIFFRACTION100
2.7852-2.8750.3552472064451400.2912515699671285X-RAY DIFFRACTION100
2.875-2.97780.3271840131851400.2946444594351268X-RAY DIFFRACTION100
2.9778-3.0970.346591759931400.2985200026231278X-RAY DIFFRACTION100
3.097-3.23790.3853468361071430.2862491470591297X-RAY DIFFRACTION100
3.2379-3.40860.3189883579021410.2823621698831291X-RAY DIFFRACTION100
3.4086-3.62210.2621620907081410.2597633397251285X-RAY DIFFRACTION100
3.6221-3.90160.3262718113951440.2415533395051310X-RAY DIFFRACTION100
3.9016-4.29410.2562131953621420.2205715691741298X-RAY DIFFRACTION100
4.2941-4.91490.2476859920311460.1931595058171327X-RAY DIFFRACTION100
4.9149-6.19030.2687104287511470.2381169935471337X-RAY DIFFRACTION100
6.1903-48.9010.2207611770931560.2109232234831424X-RAY DIFFRACTION99.8104864182

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