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- PDB-8i8z: Structure of flavone 4'-O-glucoside 7-O-glucosyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 8i8z
TitleStructure of flavone 4'-O-glucoside 7-O-glucosyltransferase from Nemophila menziesii, apo form
ComponentsGlycosyltransferase
KeywordsPLANT PROTEIN / flavone
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 / Glycosyltransferase
Function and homology information
Biological speciesNemophila menziesii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4762
Polymers54,3801
Non-polymers961
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-16 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.799, 75.151, 117.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glycosyltransferase


Mass: 54380.074 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 4000, Tris-HCl, 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: Mar 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→46.38 Å / Num. obs: 20008 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 33.69 Å2 / Rrim(I) all: 0.153 / Net I/σ(I): 13.9
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 1920 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.38 Å / SU ML: 0.293 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.6802 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2496 1996 10 %
Rwork0.1983 17961 -
obs0.2035 19957 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.34 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 5 81 3596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083595
X-RAY DIFFRACTIONf_angle_d0.97134872
X-RAY DIFFRACTIONf_chiral_restr0.0532545
X-RAY DIFFRACTIONf_plane_restr0.0062622
X-RAY DIFFRACTIONf_dihedral_angle_d3.23342181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.33411350.27821214X-RAY DIFFRACTION95.74
2.46-2.530.33631390.2581255X-RAY DIFFRACTION99.71
2.53-2.60.3011400.23341257X-RAY DIFFRACTION99.86
2.6-2.690.29171420.23551279X-RAY DIFFRACTION99.86
2.69-2.780.31091400.22821262X-RAY DIFFRACTION100
2.78-2.890.2851410.22471268X-RAY DIFFRACTION100
2.89-3.020.28841420.2311280X-RAY DIFFRACTION100
3.02-3.180.29621410.22781261X-RAY DIFFRACTION99.93
3.18-3.380.25491410.1961275X-RAY DIFFRACTION100
3.38-3.640.24131430.18351284X-RAY DIFFRACTION100
3.64-4.010.23931450.17771303X-RAY DIFFRACTION100
4.01-4.590.20371440.15641300X-RAY DIFFRACTION100
4.59-5.780.19111480.17331331X-RAY DIFFRACTION100
5.78-46.380.22641550.19451392X-RAY DIFFRACTION99.87

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