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- PDB-8hok: crystal structure of UGT71AP2 -

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Basic information

Entry
Database: PDB / ID: 8hok
Titlecrystal structure of UGT71AP2
ComponentsUGT71AP2
KeywordsTRANSFERASE / glycosyltransferase
Biological speciesScutellaria baicalensis (Baikal skullcap)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, Z.L. / He, C. / Li, F. / Qiao, X. / Ye, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Pharm Sin B / Year: 2024
Title: Functional characterization, structural basis, and protein engineering of a rare flavonoid 2'- O -glycosyltransferase from Scutellaria baicalensis .
Authors: Wang, Z. / Du, X. / Ye, G. / Wang, H. / Liu, Y. / Liu, C. / Li, F. / Agren, H. / Zhou, Y. / Li, J. / He, C. / Guo, D.A. / Ye, M.
History
DepositionDec 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UGT71AP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9954
Polymers51,6161
Non-polymers3793
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.470, 95.170, 133.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-801-

HOH

21A-817-

HOH

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Components

#1: Protein UGT71AP2


Mass: 51616.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scutellaria baicalensis (Baikal skullcap)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 0.1 MMES pH6.0, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→77.426 Å / Num. obs: 26741 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.8 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.123 / Rsym value: 0.113 / Net I/av σ(I): 5.6 / Net I/σ(I): 11.8 / Num. measured all: 178458
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.15-2.2770.5041.52702338690.2030.5440.504499.9
2.27-2.46.50.3612.12366636380.1520.3930.3615.299.9
2.4-2.576.10.272.82104134320.1170.2950.276.499.2
2.57-2.7870.2043.62248831980.0820.220.2049100
2.78-3.046.90.1375.32045629600.0550.1480.13712100
3.04-3.46.30.0947.61686426860.040.1020.09414.899.5
3.4-3.937.30.0699.41743124000.0270.0740.06920.6100
3.93-4.816.40.05910.21288620260.0250.0640.05922.499.5
4.81-6.86.90.0689.11101315980.0270.0730.06823.399.9
6.8-77.42660.0568.755909340.0240.0610.05623.499.7

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACW

2acw


Resolution: 2.15→66.31 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 1324 4.95 %
Rwork0.1625 25403 -
obs0.165 26727 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.39 Å2 / Biso mean: 30.3833 Å2 / Biso min: 6 Å2
Refinement stepCycle: final / Resolution: 2.15→66.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 24 228 3859
Biso mean--37.6 34.49 -
Num. residues----462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.240.24791400.180927892929100
2.24-2.340.23421440.174527902934100
2.34-2.460.26051510.16782776292799
2.46-2.620.24711290.16852798292799
2.62-2.820.22911500.163728212971100
2.82-3.10.19261490.157628022951100
3.1-3.550.20931670.160428012968100
3.55-4.470.1921550.139928543009100
4.47-66.310.20551390.17622972311199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9893-0.4508-0.11670.4044-0.13630.2046-0.1115-0.5807-0.08130.13220.18640.0615-0.1570.02890.04790.17120.00510.02920.22790.03910.1815-18.34140.3609-17.3699
20.3088-0.1395-0.30380.5562-0.1820.7818-0.0585-0.8492-0.17420.33280.0879-0.0088-0.0560.0867-0.00180.2424-0.00080.0420.46440.06240.2086-20.68442.3988-9.4483
30.58560.46520.21040.7922-0.31860.6007-0.2014-0.24850.08610.09990.21780.375-0.0582-0.23540.01020.23360.02420.03160.194-0.00930.1948-27.08038.8524-22.7296
40.82490.02520.32560.4454-0.38860.9669-0.090.0096-0.0068-0.10470.12250.1336-0.1272-0.17010.00060.19450.01550.00960.17440.02830.1719-30.6751-12.1458-39.5832
50.56310.7406-0.22640.9456-0.07650.29960.0646-0.12270.01220.2143-0.2058-0.1697-0.35710.1984-0.09550.1619-0.00990.04070.13290.01040.1306-15.525-13.45-22.2514
60.48190.0562-0.48720.2119-0.48281.8690.0915-0.00470.13510.0217-0.03460.02630.0284-0.25260.00060.1299-0.01530.00040.16160.01010.1671-32.7368-32.3461-13.1156
70.3013-0.13-0.06920.1931-0.02620.8690.1449-0.1686-0.0520.2313-0.0903-0.02130.053-0.16490.0010.2073-0.03510.01390.19490.01330.1524-33.4679-33.2646-7.3048
80.4890.1566-0.13940.09730.14290.49240.0502-0.03090.0402-0.0377-0.0653-0.0998-0.01970.1045-0.00010.11860.01220.01810.10640.0310.137-22.2603-24.1921-23.7463
90.54970.4988-0.23481.5114-0.32060.68330.0252-0.0592-0.0495-0.0571-0.1032-0.08650.05280.0997-0.02130.08470.02090.01970.1320.00830.1075-18.81-20.8939-24.5485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 30 )A2 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 65 )A31 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 131 )A66 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 199 )A132 - 199
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 255 )A200 - 255
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 304 )A256 - 304
7X-RAY DIFFRACTION7chain 'A' and (resid 305 through 338 )A305 - 338
8X-RAY DIFFRACTION8chain 'A' and (resid 339 through 391 )A339 - 391
9X-RAY DIFFRACTION9chain 'A' and (resid 392 through 463 )A392 - 463

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