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- PDB-8in7: Crystal structure of UGT74AN3-UDP -

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Basic information

Entry
Database: PDB / ID: 8in7
TitleCrystal structure of UGT74AN3-UDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase
Function / homologyquercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glycosyltransferase
Function and homology information
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFeng, L. / Wei, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of UGT74AN3-UDP
Authors: Wei, H. / Wei, H.
History
DepositionMar 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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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)54,1392
Polymers53,5721
Non-polymers5661
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-7 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.437, 52.068, 200.195
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 Glycosyltransferase


Mass: 53572.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A385Z961, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG2000MME, 0.1M Hepes (7.5), potassium nitro

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→46.19 Å / Num. obs: 38464 / % possible obs: 82.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 20.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 25.2
Reflection shellResolution: 1.9→1.94 Å / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHENIXmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.19 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 1917 4.98 %
Rwork0.1845 --
obs0.1864 38464 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 0 301 3743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083520
X-RAY DIFFRACTIONf_angle_d0.9894777
X-RAY DIFFRACTIONf_dihedral_angle_d10.104449
X-RAY DIFFRACTIONf_chiral_restr0.061555
X-RAY DIFFRACTIONf_plane_restr0.008592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30431350.25322532X-RAY DIFFRACTION100
1.95-20.23551150.19732613X-RAY DIFFRACTION100
2-2.060.21841440.17692550X-RAY DIFFRACTION100
2.06-2.130.25171390.1762520X-RAY DIFFRACTION100
2.13-2.20.21441370.17982593X-RAY DIFFRACTION100
2.2-2.290.26661230.1942605X-RAY DIFFRACTION100
2.29-2.390.23711370.19042601X-RAY DIFFRACTION100
2.39-2.520.21671420.18872574X-RAY DIFFRACTION100
2.52-2.680.24551470.18852587X-RAY DIFFRACTION100
2.68-2.880.26591280.19162613X-RAY DIFFRACTION100
2.88-3.170.23731270.18772628X-RAY DIFFRACTION100
3.18-3.630.19971380.17812642X-RAY DIFFRACTION100
3.63-4.580.19371580.16052669X-RAY DIFFRACTION100
4.58-46.190.19851470.19082820X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.3528 Å / Origin y: 20.3331 Å / Origin z: 74.8492 Å
111213212223313233
T0.111 Å20.0066 Å20.0099 Å2-0.1284 Å2-0.028 Å2--0.1404 Å2
L1.7703 °2-0.1782 °2-0.3738 °2-0.8023 °20.2204 °2--1.6824 °2
S0.0101 Å °-0.304 Å °0.2137 Å °-0.0199 Å °0.0305 Å °-0.0134 Å °-0.1142 Å °0.0132 Å °-0.0114 Å °
Refinement TLS groupSelection details: all

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