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- PDB-7cyw: Crystal structure of a flavonoid C-glucosyltrasferase from Fagopy... -

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Basic information

Entry
Database: PDB / ID: 7cyw
TitleCrystal structure of a flavonoid C-glucosyltrasferase from Fagopyrum esculentum (FeCGTa) complexed with BrUTP
ComponentsUDP-glycosyltransferase 708C1
KeywordsTRANSFERASE / flavonoid C-glucosyltransferase / glycosyltransferase / C-glycosylation
Function / homology2-hydroxyflavanone C-glucosyltransferase / UDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / ACETATE ION / 5-bromouridine 5'-(tetrahydrogen triphosphate) / UDP-glycosyltransferase 708C1
Function and homology information
Biological speciesFagopyrum esculentum (common buckwheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKoyanagi, Y. / Taguchi, G. / Arai, R.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP26450120 Japan
Japan Society for the Promotion of Science (JSPS)JP20K05825 Japan
Japan Society for the Promotion of Science (JSPS)JP24780097 Japan
Japan Society for the Promotion of Science (JSPS)JP16K05841 Japan
Citation
Journal: To be published
Title: Crystal structure of a flavonoid C-glucosyltrasferase from Fagopyrum esculentum
Authors: Koyanagi, Y. / Arai, R. / Taguchi, G.
#1: Journal: Plant J. / Year: 2014
Title: Purification, molecular cloning and functional characterization of flavonoid C-glucosyltransferases from Fagopyrum esculentum M. (buckwheat) cotyledon.
Authors: Nagatomo, Y. / Usui, S. / Ito, T. / Kato, A. / Shimosaka, M. / Taguchi, G.
History
DepositionSep 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glycosyltransferase 708C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5703
Polymers48,9481
Non-polymers6222
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-1 kcal/mol
Surface area18000 Å2
Unit cell
Length a, b, c (Å)53.565, 76.010, 93.194
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-glycosyltransferase 708C1 / C-glucosyltransferase a / FeCGTa / UDP-glucose:2-hydroxyflavanone C-glucosyltransferase


Mass: 48947.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fagopyrum esculentum (common buckwheat)
Gene: UGT708C1, CGTa / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: A0A0A1HA03, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-BUP / 5-bromouridine 5'-(tetrahydrogen triphosphate)


Mass: 563.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14BrN2O15P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 23% PEG 8000, 100 mM MES/Sodium hydroxyde, 300 mM Calcium acetate

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.91983 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 15, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91983 Å / Relative weight: 1
ReflectionResolution: 1.797→50 Å / Num. obs: 35650 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.18 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.053 / Rrim(I) all: 0.138 / Χ2: 0.988 / Net I/av σ(I): 14.43 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.866.31.0072.2935230.7750.4271.0960.97599.4
1.86-1.946.30.67235490.8560.2830.7310.99999.5
1.94-2.036.50.435200.9190.1670.4340.99799.5
2.03-2.136.60.2735340.9630.1120.2931.01599.6
2.13-2.276.70.20635830.9790.0840.2231.01399.8
2.27-2.4470.16535890.9870.0670.1780.98599.9
2.44-2.697.20.13935800.990.0550.1490.996100
2.69-3.087.30.12236140.9910.0490.1320.966100
3.08-3.8870.10236490.9860.0420.110.96899.4
3.88-506.30.0835090.9920.0350.0880.97591.6

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Processing

Software
NameVersionClassification
DENZOdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MR-Rosettaphasing
Cootmodel building
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VCH

2vch


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.68 / SU ML: 0.113 / SU R Cruickshank DPI: 0.1618 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1774 5 %RANDOM
Rwork0.2014 ---
obs0.2033 33754 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 98.68 Å2 / Biso mean: 33.13 Å2 / Biso min: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å20 Å2
2---0.62 Å20 Å2
3---2.3 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 34 273 3637
Biso mean--27.36 39.21 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193476
X-RAY DIFFRACTIONr_bond_other_d0.0060.023279
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9674735
X-RAY DIFFRACTIONr_angle_other_deg0.9653.0027584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13323.972141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5515562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8841515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213848
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02779
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 108 -
Rwork0.285 2469 -
all-2577 -
obs--97.98 %

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