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- PDB-8hoj: Crystal structure of UGT71AP2 in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 8hoj
TitleCrystal structure of UGT71AP2 in complex with UDP
ComponentsUGT71AP2
KeywordsTRANSFERASE / glycosyltransferase
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesScutellaria baicalensis (Baikal skullcap)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

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Assembly

Deposited unit
A: UGT71AP2
B: UGT71AP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0404
Polymers103,2322
Non-polymers8082
Water00
1
A: UGT71AP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0202
Polymers51,6161
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-8 kcal/mol
Surface area19910 Å2
MethodPISA
2
B: UGT71AP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0202
Polymers51,6161
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-9 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.728, 108.544, 84.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein UGT71AP2


Mass: 51616.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scutellaria baicalensis (Baikal skullcap)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
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: 47.03 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 21963 / % possible obs: 99.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 50.43 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.063 / Rrim(I) all: 0.137 / Χ2: 0.962 / Net I/σ(I): 4.7 / Num. measured all: 100532
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.954.70.79110670.8220.410.8950.93799.8
2.95-34.70.76510970.7630.3960.8660.96999.9
3-3.064.60.6510730.7850.340.7370.97399.9
3.06-3.124.50.55110700.8190.2940.6280.92999.8
3.12-3.194.30.44810820.850.2460.5140.94199.6
3.19-3.274.50.40810930.8920.2170.4650.93599.7
3.27-3.354.40.36810680.9170.1970.4190.90699.9
3.35-3.444.90.34310840.8960.1730.3861.00199.9
3.44-3.544.90.25910970.9540.1310.2911.018100
3.54-3.654.90.20210770.9710.1020.2271.00299.9
3.65-3.784.80.17210850.9850.0870.1931.034100
3.78-3.944.80.13910990.9840.070.1561.01899.7
3.94-4.114.70.11610960.990.0590.131.041100
4.11-4.334.60.09111000.990.0470.1030.99599.8
4.33-4.64.20.07710900.9920.0410.0880.98399.5
4.6-4.964.30.0711020.9940.0370.0790.99598.5
4.96-5.454.70.07311080.9950.0370.0830.95100
5.45-6.244.70.07411240.9940.0370.0830.89299.9
6.24-7.854.50.05911430.9960.0310.0670.84199.8
7.85-4040.03912080.9970.0210.0450.86499.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
DENZOdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACW

2acw


Resolution: 2.9→27.46 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2844 969 4.98 %
Rwork0.2256 18502 -
obs0.2287 19471 88.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.27 Å2 / Biso mean: 54.4715 Å2 / Biso min: 9.68 Å2
Refinement stepCycle: final / Resolution: 2.9→27.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6847 0 50 0 6897
Biso mean--63.44 --
Num. residues----884
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.050.3297800.26361606168655
3.05-3.240.31731070.27872191229875
3.24-3.490.32431620.27412730289293
3.49-3.840.33341650.24472917308299
3.84-4.40.26711570.217629573114100
4.4-5.530.26081300.20613000313099
5.53-27.460.2491680.19443101326999

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