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- PDB-7c2x: Crystal Structure of Glycyrrhiza uralensis UGT73P12 complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7c2x
TitleCrystal Structure of Glycyrrhiza uralensis UGT73P12 complexed with glycyrrhetinic acid 3-O-monoglucuronide
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / UDP-glucuronosyltransferase / GT-B fold / Glycyrrhizin synthesis
Function / homologyUDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / Chem-FJL / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesGlycyrrhiza uralensis (Chinese licorice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRen, J.
CitationJournal: To Be Published
Title: Crystal Structure of Glycyrrhiza uralensis UGT73P12 complexed with glycyrrhetinic acid 3-O-monoglucuronide
Authors: Ren, J. / Liu, M.
History
DepositionMay 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: 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: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8923
Polymers57,8411
Non-polymers1,0512
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-10 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.465, 84.425, 92.836
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 Glycosyltransferase /


Mass: 57840.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycyrrhiza uralensis (Chinese licorice)
Gene: UGT73P12 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A5A4WN00, Transferases; Glycosyltransferases; Hexosyltransferases
#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 / Comment: UDP*YM
#3: Chemical ChemComp-FJL / (2~{S},3~{S},4~{S},5~{R},6~{R})-6-[[(3~{S},4~{a}~{R},6~{a}~{R},6~{b}~{S},8~{a}~{S},11~{S},12~{a}~{R},14~{a}~{R},14~{b}~{S})-11-carboxy-4,4,6~{a},6~{b},8~{a},11,14~{b}-heptamethyl-14-oxidanylidene-2,3,4~{a},5,6,7,8,9,10,12,12~{a},14~{a}-dodecahydro-1~{H}-picen-3-yl]oxy]-3,4,5-tris(oxidanyl)oxane-2-carboxylic acid


Mass: 646.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H54O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, sodium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 41730 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.027 / Rrim(I) all: 0.062 / Χ2: 1.017 / Net I/σ(I): 14.7 / Num. measured all: 238254
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88-1.954.70.22740900.9630.1170.2560.74399.4
1.95-2.035.20.17441280.9780.0850.1940.88899.7
2.03-2.1260.13741250.9860.0620.1511.07299.7
2.12-2.236.30.11141270.9910.0490.1211.06999.7
2.23-2.3760.0941310.9930.0410.0991.06799.4
2.37-2.556.30.07641680.9950.0340.0831.0399.8
2.55-2.8160.06141810.9960.0280.0671.08699.8
2.81-3.216.10.05442020.9960.0250.061.08799.8
3.21-4.055.70.04642160.9970.0220.0511.02799.4
4.05-504.90.03943620.9980.020.0450.99298

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O87

6o87


Resolution: 1.89→26.75 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 2144 5.15 %
Rwork0.1835 39512 -
obs0.1856 41656 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.86 Å2 / Biso mean: 27.446 Å2 / Biso min: 11.9 Å2
Refinement stepCycle: final / Resolution: 1.89→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 71 303 4263
Biso mean--34 30.57 -
Num. residues----490
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.930.26391120.20042392250490
1.93-1.980.2311670.193325792746100
1.98-2.030.26721420.197426052747100
2.03-2.090.24011430.188826172760100
2.09-2.160.241650.183226232788100
2.16-2.240.24481390.189626382777100
2.24-2.330.23111280.19082649277799
2.33-2.430.26121550.195326122767100
2.43-2.560.23541450.197526252770100
2.56-2.720.23621440.19626732817100
2.72-2.930.23791490.19926292778100
2.93-3.220.24811200.202227062826100
3.22-3.690.20481490.177826892838100
3.69-4.640.17531370.15832692282999
4.64-26.750.22091490.17112783293298

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