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- PDB-7zf0: Crystal structure of UGT85B1 from Sorghum bicolor in complex with... -

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Basic information

Entry
Database: PDB / ID: 7zf0
TitleCrystal structure of UGT85B1 from Sorghum bicolor in complex with UDP and p-hydroxymandelonitrile
ComponentsCyanohydrin beta-glucosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / cyanogenic / dhurrin biosynthesis / GT-B fold
Function / homologycyanohydrin beta-glucosyltransferase / dhurrin biosynthetic process / cyanohydrin beta-glucosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / endoplasmic reticulum membrane / (2S)-HYDROXY(4-HYDROXYPHENYL)ETHANENITRILE / URIDINE-5'-DIPHOSPHATE / Cyanohydrin beta-glucosyltransferase
Function and homology information
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPutkaradze, N. / Fredslund, F. / Welner, D.H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20CC0035580 Denmark
Citation
Journal: Plant J. / Year: 2022
Title: Structure-guided engineering of key amino acids in UGT85B1 controlling substrate and stereo-specificity in aromatic cyanogenic glucoside biosynthesis.
Authors: Del Giudice, R. / Putkaradze, N. / Dos Santos, B.M. / Hansen, C.C. / Crocoll, C. / Motawia, M.S. / Fredslund, F. / Laursen, T. / Welner, D.H.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanohydrin beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,91012
Polymers53,7991
Non-polymers1,11211
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint25 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.630, 91.380, 92.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cyanohydrin beta-glucosyltransferase / / UDP-glucose-p-hydroxymandelonitrile glucosyltransferase


Mass: 53798.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: UGT85B1, HMNGT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SBL1, cyanohydrin beta-glucosyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DHR / (2S)-HYDROXY(4-HYDROXYPHENYL)ETHANENITRILE


Mass: 149.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES/imidazole, 12.5% (w/v) PEG8000, 12.5% (v/v) ethylene glycol, 120 mM MORPHEUS monosaccharides mix

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2020
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.5→45.69 Å / Num. obs: 104591 / % possible obs: 99.86 % / Redundancy: 5.6 % / Biso Wilson estimate: 29.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.55
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 10304 / CC1/2: 0.329

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZER

7zer


Resolution: 1.5→45.69 Å / SU ML: 0.2392 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2097 5131 4.91 %
Rwork0.1885 99460 -
obs0.1896 104591 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.85 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3599 0 72 329 4000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033743
X-RAY DIFFRACTIONf_angle_d1.07085082
X-RAY DIFFRACTIONf_chiral_restr0.0735572
X-RAY DIFFRACTIONf_plane_restr0.0111657
X-RAY DIFFRACTIONf_dihedral_angle_d14.45291341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.510.44551560.44892834X-RAY DIFFRACTION87.55
1.51-1.530.43981620.42453335X-RAY DIFFRACTION99.86
1.53-1.550.3941860.38423259X-RAY DIFFRACTION99.94
1.55-1.570.39811520.35063320X-RAY DIFFRACTION99.94
1.57-1.590.32631560.33423290X-RAY DIFFRACTION99.97
1.59-1.610.30761760.30393263X-RAY DIFFRACTION99.97
1.61-1.640.31711670.29193323X-RAY DIFFRACTION100
1.64-1.660.29131690.27633320X-RAY DIFFRACTION100
1.66-1.690.27461720.27343265X-RAY DIFFRACTION99.94
1.69-1.710.27331960.26813292X-RAY DIFFRACTION99.94
1.71-1.740.26641610.25213309X-RAY DIFFRACTION100
1.74-1.780.23031630.23223309X-RAY DIFFRACTION99.97
1.78-1.810.25761740.22193305X-RAY DIFFRACTION99.97
1.81-1.850.23681740.21163318X-RAY DIFFRACTION100
1.85-1.890.25131810.20593287X-RAY DIFFRACTION99.94
1.89-1.930.22651660.20313314X-RAY DIFFRACTION99.97
1.93-1.980.21011650.20413324X-RAY DIFFRACTION100
1.98-2.030.22271680.19993324X-RAY DIFFRACTION99.97
2.03-2.090.231520.20843335X-RAY DIFFRACTION100
2.09-2.160.24121780.20443326X-RAY DIFFRACTION100
2.16-2.240.23511740.19483327X-RAY DIFFRACTION99.97
2.24-2.330.19431770.1833347X-RAY DIFFRACTION100
2.33-2.430.22781830.183302X-RAY DIFFRACTION100
2.43-2.560.19392040.17823332X-RAY DIFFRACTION99.94
2.56-2.720.17281820.17493338X-RAY DIFFRACTION100
2.72-2.930.19521690.17483351X-RAY DIFFRACTION100
2.93-3.230.20391430.18613409X-RAY DIFFRACTION100
3.23-3.690.24011670.17893408X-RAY DIFFRACTION100
3.69-4.650.16571760.15473438X-RAY DIFFRACTION99.94
4.65-45.690.18351820.17463556X-RAY DIFFRACTION99.28

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