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- PDB-6l5q: crystal structure of GgCGT in complex with UDP-Gal -

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Basic information

Entry
Database: PDB / ID: 6l5q
Titlecrystal structure of GgCGT in complex with UDP-Gal
ComponentsGgCGT
KeywordsTRANSFERASE / di-C-glycosyltransferase
Function / homologyGlycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GALACTOSE-URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesGlycyrrhiza glabra (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.894 Å
AuthorsZhang, M. / Li, F.D. / Ye, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Functional Characterization and Structural Basis of an Efficient Di-C-glycosyltransferase fromGlycyrrhiza glabra.
Authors: Zhang, M. / Li, F.D. / Li, K. / Wang, Z.L. / Wang, Y.X. / He, J.B. / Su, H.F. / Zhang, Z.Y. / Chi, C.B. / Shi, X.M. / Yun, C.H. / Zhang, Z.Y. / Liu, Z.M. / Zhang, L.R. / Yang, D.H. / Ma, M. / Qiao, X. / Ye, M.
History
DepositionOct 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: GgCGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6592
Polymers52,0931
Non-polymers5661
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-9 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.827, 139.278, 73.822
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GgCGT


Mass: 52093.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycyrrhiza glabra (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Tris, pH 8.5, 25% w/v Polyethylene glycol 3350

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.894→40 Å / Num. obs: 9820 / % possible obs: 96.2 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.058 / Rrim(I) all: 0.185 / Χ2: 0.997 / Net I/σ(I): 3.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.957.50.7373870.6980.2670.7880.87278
2.95-37.80.7533990.5530.2750.8060.9181.6
3-3.068.40.7864520.6710.2790.8370.93986.9
3.06-3.128.70.6414400.8130.2210.6810.96491.3
3.12-3.1990.6244660.7580.2150.6630.96893
3.19-3.279.30.5724890.8660.1940.6060.93896.6
3.27-3.359.60.5245020.8550.1750.5540.94997.5
3.35-3.449.60.4654930.9230.1550.4910.98699
3.44-3.549.60.4414920.9350.1480.4670.99299.2
3.54-3.6590.3325070.9410.1150.3521.0599.8
3.65-3.789.60.2755000.9690.0920.2911.062100
3.78-3.9410.70.2725160.9760.0860.2851.064100
3.94-4.1110.80.2365150.990.0740.2481.059100
4.11-4.33110.1855070.9910.0580.1941.039100
4.33-4.610.80.165080.9910.050.1681.059100
4.6-4.9610.50.145120.9940.0440.1471.07599.8
4.96-5.459.40.1455140.9920.0490.1531.046100
5.45-6.2410.50.1325190.9940.0420.1390.972100
6.24-7.8510.50.1065340.9950.0340.1120.931100
7.85-409.20.0735680.9970.0250.0780.929100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACW

2acw


Resolution: 2.894→36.911 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.44
RfactorNum. reflection% reflection
Rfree0.2765 397 4.81 %
Rwork0.2262 --
obs0.2285 8250 80.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.18 Å2 / Biso mean: 48.7239 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 2.894→36.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 36 0 3365
Biso mean--46.86 --
Num. residues----432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8943-3.31290.3246800.286170854
3.3129-4.1730.30321440.2362285589
4.173-36.9110.24861730.2064329099
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)
11.9399-0.1480.21471.81430.45361.5603-0.04820.2286-0.63530.219-0.02880.42490.53130.16340.05120.29950.11760.03460.33370.0280.4258-22.958-32.506-11.8658
21.6493-0.9157-1.33632.78270.83874.4725-0.0877-0.4166-0.00670.1249-0.12150.92230.241-0.89810.13010.18560.04570.01790.51260.06780.5546-35.3855-10.05881.7369
31.6239-0.2702-0.58911.79651.04610.7256-0.1106-0.47-0.35040.61030.0150.42590.50340.0820.04020.33420.04520.0750.36040.11910.2677-23.1369-22.98261.4028
40.79750.081-0.26930.179-0.42411.010.24160.14060.2428-0.3199-0.0071-0.3197-0.25550.16960.62310.38860.02530.20650.506-0.14840.3478-8.2566-10.1499-25.1427
54.1088-1.50221.8894.95230.67935.19250.5337-0.20640.2323-0.0975-0.1530.4027-0.22930.1342-0.31560.45230.04570.0980.4818-0.01810.212-22.1074-0.7299-28.0759
61.5899-0.0073-0.53930.98290.19251.81550.0952-0.28050.0489-0.08360.1419-0.2498-0.09390.28370.07270.19630.02010.09140.3789-0.05250.1238-16.1053-9.168-10.8333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 162 )A16 - 162
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 197 )A163 - 197
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 251 )A198 - 251
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 281 )A252 - 281
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 345 )A282 - 345
6X-RAY DIFFRACTION6chain 'A' and (resid 346 through 469 )A346 - 469

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