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- PDB-2vce: Characterization and engineering of the bifunctional N- and O- gl... -

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Basic information

Entry
Database: PDB / ID: 2vce
TitleCharacterization and engineering of the bifunctional N- and O- glucosyltransferase involved in xenobiotic metabolism in plants
ComponentsHYDROQUINONE GLUCOSYLTRANSFERASE
KeywordsTRANSFERASE / N-GLUCOSYLTRANSFERASE / S-GLUCOSYLTRANSFERASE / GLYCOSYLTRANSFERASE / PLANT GLYCOSYLATION / N-GLYCOSYLATION / O-GLYCOSYLATION / O- GLUCOSYLTRANSFERASE / UDP-GLUCOSE- DEPENDENT
Function / homology
Function and homology information


hydroquinone glucosyltransferase / hydroquinone glucosyltransferase activity / lignin biosynthetic process / UDP-glucosyltransferase activity / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / xenobiotic catabolic process / xenobiotic metabolic process / response to toxic substance
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
2,4,5-trichlorophenol / Chem-U2F / UDP-glycosyltransferase 72B1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrazier-Hicks, M. / Offen, W.A. / Gershater, M.C. / Revett, T.J. / Lim, E.K. / Bowles, D.J. / Davies, G.J. / Edwards, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Characterization and Engineering of the Bifunctional N- and O-Glucosyltransferase Involved in Xenobiotic Metabolism in Plants.
Authors: Brazier-Hicks, M. / Offen, W.A. / Gershater, M.C. / Revett, T.J. / Lim, E.K. / Bowles, D.J. / Davies, G.J. / Edwards, R.
History
DepositionSep 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROQUINONE GLUCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8204
Polymers52,9931
Non-polymers8283
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.807, 94.335, 57.059
Angle α, β, γ (deg.)90.00, 110.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYDROQUINONE GLUCOSYLTRANSFERASE / ARBUTIN SYNTHASE / UGT72B1


Mass: 52992.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET-30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER
References: UniProt: Q9M156, hydroquinone glucosyltransferase
#2: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#3: Chemical ChemComp-TC7 / 2,4,5-trichlorophenol


Mass: 197.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H3Cl3O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 25 % (W/V) PEG 3350, 0.1 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→19.67 Å / Num. obs: 37280 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VCH

2vch


Resolution: 1.9→19.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.951 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5, 251-255, 317-320 AND 477-480 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1865 5.1 %RANDOM
Rwork0.158 ---
obs0.16 35036 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.26 Å2
2--1.1 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3571 0 50 402 4023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223786
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6472.0015170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69923.506154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41915628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5031526
X-RAY DIFFRACTIONr_chiral_restr0.1110.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022848
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21898
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22557
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2370
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0191.52414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61123803
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57431575
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7054.51356
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 135
Rwork0.196 2410

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