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- PDB-7w0z: Glycosyltranferase UGT74AN2 -

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Basic information

Entry
Database: PDB / ID: 7w0z
TitleGlycosyltranferase UGT74AN2
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Complex with resibufagenin
Function / homology
Function and homology information


UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
Chem-6JI / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCalotropis gigantea (mudar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWei, H. / Feng, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2022
Title: Functional and Structural Dissection of a Plant Steroid 3-O-Glycosyltransferase Facilitated the Engineering Enhancement of Sugar Donor Promiscuity
Authors: Huang, W. / He, Y. / Jiang, R. / Deng, Z. / Long, F.
History
DepositionNov 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7413
Polymers53,9521
Non-polymers7892
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-9 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.026, 76.553, 63.553
Angle α, β, γ (deg.)90.000, 96.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycosyltransferase / Plant steroid glycosyltransferase UGT74AN2


Mass: 53952.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calotropis gigantea (mudar) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A385Z7H9
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-6JI / 5-[(1R,2S,4R,6R,7R,10S,11S,14S,16R)-14-hydroxy-7,11-dimethyl-3-oxapentacyclo[8.8.0.02,4.02,7.011,16]octadecan-6-yl]pyran-2-one / Resibufogenin


Mass: 384.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, 0.1M sodium chloride, 0.1M MES (pH 6.5)

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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→48.69 Å / Num. obs: 38306 / % possible obs: 99.9 % / Redundancy: 17.7 % / Biso Wilson estimate: 21.91 Å2 / CC1/2: 0.956 / Net I/σ(I): 11.5
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2415 / CC1/2: 0.733

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L8Z

6l8z


Resolution: 2.1→42.24 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 1455 5.13 %
Rwork0.1884 26933 -
obs0.1905 28388 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.43 Å2 / Biso mean: 22.728 Å2 / Biso min: 9.28 Å2
Refinement stepCycle: final / Resolution: 2.1→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 53 46 3437
Biso mean--40.22 19.58 -
Num. residues----439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.180.25181460.194526682814100
2.18-2.260.25621500.195826882838100
2.26-2.370.23571320.203926862818100
2.37-2.490.28451420.200426932835100
2.49-2.650.25361380.205426862824100
2.65-2.850.24241560.211926952851100
2.85-3.140.23471360.201426662802100
3.14-3.590.23951660.19162679284599
3.59-4.520.19951420.16527172859100
4.52-42.240.19371470.17227552902100
Refinement TLS params.Method: refined / Origin x: 39.3571 Å / Origin y: 27.4822 Å / Origin z: 42.3791 Å
111213212223313233
T0.1204 Å20.0202 Å2-0.0001 Å2-0.1058 Å2-0.0159 Å2--0.1127 Å2
L0.491 °20.2526 °20.1994 °2-0.4304 °20.3887 °2--0.5027 °2
S-0.0308 Å °-0.0484 Å °0.0033 Å °-0.0446 Å °-0.0237 Å °-0.0089 Å °-0.0395 Å °-0.0379 Å °-0.0041 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 477
2X-RAY DIFFRACTION1allA501 - 502
3X-RAY DIFFRACTION1allS1 - 293

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