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- PDB-8i90: Structure of flavone 4'-O-glucoside 7-O-glucosyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 8i90
TitleStructure of flavone 4'-O-glucoside 7-O-glucosyltransferase from Nemophila menziesii, complex with UDP-glucose
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 / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glycosyltransferase
Function and homology information
Biological speciesNemophila menziesii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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)109,8934
Polymers108,7602
Non-polymers1,1332
Water3,225179
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9462
Polymers54,3801
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-9 kcal/mol
Surface area19020 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9462
Polymers54,3801
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-8 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.654, 74.928, 112.404
Angle α, β, γ (deg.)90.000, 92.943, 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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
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: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→48.82 Å / Num. obs: 51488 / % possible obs: 95.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 30.23 Å2 / Rrim(I) all: 0.17 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 5068 / CC1/2: 0.806

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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: 2.1→48.82 Å / SU ML: 0.3086 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.246 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2832 2002 3.9 %
Rwork0.2296 49356 -
obs0.2318 51358 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 0 72 179 7238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087227
X-RAY DIFFRACTIONf_angle_d0.9759806
X-RAY DIFFRACTIONf_chiral_restr0.05591102
X-RAY DIFFRACTIONf_plane_restr0.00641237
X-RAY DIFFRACTIONf_dihedral_angle_d3.2574346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.3781380.28923325X-RAY DIFFRACTION89.6
2.15-2.210.30331370.2563559X-RAY DIFFRACTION95.93
2.21-2.280.32591540.24073540X-RAY DIFFRACTION96.85
2.28-2.350.32771390.24343576X-RAY DIFFRACTION96.8
2.35-2.430.31341450.23123553X-RAY DIFFRACTION96.35
2.43-2.530.27751400.24163557X-RAY DIFFRACTION95.73
2.53-2.650.31121490.24583494X-RAY DIFFRACTION95.14
2.65-2.790.34391420.25313438X-RAY DIFFRACTION92.77
2.79-2.960.2991350.24413421X-RAY DIFFRACTION92.65
2.96-3.190.36911360.24913332X-RAY DIFFRACTION90.38
3.19-3.510.28351360.23463411X-RAY DIFFRACTION90.83
3.51-4.020.2531460.20823617X-RAY DIFFRACTION97.54
4.02-5.060.24361510.19623733X-RAY DIFFRACTION99.77
5.06-48.820.23781540.23193800X-RAY DIFFRACTION99.57

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