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- PDB-8i94: Structure of flavone 4'-O-glucoside 7-O-glucosyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 8i94
TitleStructure of flavone 4'-O-glucoside 7-O-glucosyltransferase from Nemophila menziesii, complex with luteolin
ComponentsGlycosyltransferase
KeywordsPLANT PROTEIN / flavone / luteolin
Function / homologyquercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / Chem-LU2 / Glycosyltransferase
Function and homology information
Biological speciesNemophila menziesii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Shirouzu, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Molecular basis of ligand recognition specificity of flavone glucosyltransferases in Nemophila menziesii.
Authors: Murayama, K. / Kato-Murayama, M. / Hosaka, T. / Okitsu, N. / Tanaka, Y. / Shirouzu, M.
History
DepositionFeb 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5256
Polymers108,7602
Non-polymers7654
Water1,63991
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7623
Polymers54,3801
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19580 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7623
Polymers54,3801
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.975, 75.226, 119.743
Angle α, β, γ (deg.)90.000, 96.497, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycosyltransferase


Mass: 54380.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nemophila menziesii (plant) / Gene: NmF4'G7GT / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A292GEP7, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-LU2 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one / Luteolin


Mass: 286.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, Hepes, Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.43→48.33 Å / Num. obs: 35086 / % possible obs: 94.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 36.33 Å2 / Rrim(I) all: 0.222 / Net I/σ(I): 7.4
Reflection shellResolution: 2.43→2.52 Å / Num. unique obs: 3377 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→48.33 Å / SU ML: 0.3962 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 35.2474 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.3094 1999 5.7 %
Rwork0.2373 33064 -
obs0.2415 35063 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.38 Å2
Refinement stepCycle: LAST / Resolution: 2.43→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6942 0 52 91 7085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00857157
X-RAY DIFFRACTIONf_angle_d1.02039703
X-RAY DIFFRACTIONf_chiral_restr0.05391079
X-RAY DIFFRACTIONf_plane_restr0.0071232
X-RAY DIFFRACTIONf_dihedral_angle_d3.5834320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.490.36641260.29312094X-RAY DIFFRACTION84
2.49-2.560.36761450.26572388X-RAY DIFFRACTION95.58
2.56-2.630.37661460.27412395X-RAY DIFFRACTION95.92
2.63-2.720.35491410.28492346X-RAY DIFFRACTION93.99
2.72-2.820.34591430.25522371X-RAY DIFFRACTION93.84
2.82-2.930.34091440.25132361X-RAY DIFFRACTION94.17
2.93-3.060.30631380.24772311X-RAY DIFFRACTION92.91
3.06-3.220.36921410.25792325X-RAY DIFFRACTION92.67
3.22-3.430.38811400.24382326X-RAY DIFFRACTION92.19
3.43-3.690.29471380.23012286X-RAY DIFFRACTION91.4
3.69-4.060.28471420.2132333X-RAY DIFFRACTION92.39
4.06-4.650.2621460.20082416X-RAY DIFFRACTION95.14
4.65-5.860.27011530.21922518X-RAY DIFFRACTION99.44
5.86-48.330.28471560.24872594X-RAY DIFFRACTION99.67

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