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- PDB-3hbf: Structure of UGT78G1 complexed with myricetin and UDP -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3hbf
TitleStructure of UGT78G1 complexed with myricetin and UDP
ComponentsFlavonoid 3-O-glucosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / GT-B fold / GT1 / Phenylpropanoid metabolism
Function / homology
Function and homology information


phenylpropanoid metabolic process / flavonoid biosynthetic process / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MYC / URIDINE-5'-DIPHOSPHATE / Flavonoid 3-O-glucosyltransferase
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, X. / Modolo, L. / Li, L. / Dixon, R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of glycosyltransferase UGT78G1 reveal the molecular basis for glycosylation and deglycosylation of (iso)flavonoids.
Authors: Modolo, L.V. / Li, L. / Pan, H. / Blount, J.W. / Dixon, R.A. / Wang, X.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavonoid 3-O-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9383
Polymers50,2161
Non-polymers7222
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.166, 77.581, 59.554
Angle α, β, γ (deg.)90.00, 96.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flavonoid 3-O-glucosyltransferase / UDP glucose:flavonoid 3-O-glucosyltransferase / UDP-glycosyltransferase 78G1


Mass: 50215.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: GT83F, UGT78G1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A6XNC6, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN


Mass: 318.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 290 K / pH: 5.5
Details: 25% PEG 3350, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→35.82 Å / Num. obs: 25599 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.6 / % possible all: 90

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Processing

Software
NameClassification
HKL-3000data collection
PHASERphasing
CNSrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.82 Å / Rfactor Rfree error: 0.005 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2425 9.9 %RANDOM
Rwork0.196 ---
obs0.196 24486 93.9 %-
all-24486 --
Displacement parametersBiso mean: 42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 48 246 3742
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 333 9.8 %
Rwork0.255 3065 -
obs--78.1 %

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