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- PDB-2pq6: Crystal structure of Medicago truncatula UGT85H2- Insights into t... -

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Basic information

Entry
Database: PDB / ID: 2pq6
TitleCrystal structure of Medicago truncatula UGT85H2- Insights into the structural basis of a multifunctional (Iso) flavonoid glycosyltransferase
ComponentsUDP-glucuronosyl/UDP-glucosyltransferase
KeywordsTRANSFERASE / glycosylation / isoflavonoid / uridine diphosphate glycosyltransferase / Structural Genomics
Function / homology
Function and homology information


quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cytoplasm
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / 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
Glycosyltransferase / :
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, L. / Modolo, L.V. / Escamilla-Trevino, L.L. / Wang, X.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of Medicago truncatula UGT85H2 - Insights into the Structural Basis of a Multifunctional (Iso)flavonoid Glycosyltransferase.
Authors: Li, L. / Modolo, L.V. / Escamilla-Trevino, L.L. / Achnine, L. / Dixon, R.A. / Wang, X.
History
DepositionMay 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Authors state that residue at position 305 is indeed THR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucuronosyl/UDP-glucosyltransferase


Theoretical massNumber of molelcules
Total (without water)54,5581
Polymers54,5581
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.997, 82.961, 95.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-glucuronosyl/UDP-glucosyltransferase


Mass: 54557.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Plasmid: pET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q1RXH4, UniProt: A6XNC5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 20% PEG3350, 0.2M magnesium formate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 27676 / Num. obs: 27621 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 99.8 % / Biso Wilson estimate: 10.2 Å2 / Rsym value: 0.082 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 99.8 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2710 / Rsym value: 0.052 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACV

2acv


Resolution: 2.1→24.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 297161.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2096 8 %RANDOM
Rwork0.197 ---
obs0.197 26220 95.2 %-
all-27542 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6229 Å2 / ksol: 0.335367 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---2.03 Å20 Å2
3---2.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 0 252 3776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 311 7.5 %
Rwork0.236 3834 -
obs-4145 91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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