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- PDB-6l5r: crystal structure of GgCGT in complex with UDP-Glu -

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Basic information

Entry
Database: PDB / ID: 6l5r
Titlecrystal structure of GgCGT in complex with UDP-Glu
ComponentsGgCGT
KeywordsTRANSFERASE / di-C-glycosyltransferase
Function / homologyGlycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-G50 / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesGlycyrrhiza glabra (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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)52,7713
Polymers52,0931
Non-polymers6782
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-10 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.750, 67.336, 105.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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-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-G50 / 3-(4-HYDROXYPHENYL)-1-(2,4,6-TRIHYDROXYPHENYL)PROPAN-1-ONE


Mass: 274.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O5
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: 1.97 Å3/Da / Density % sol: 37.48 %
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: 2.89→40 Å / Num. obs: 9044 / % possible obs: 99.7 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.072 / Rrim(I) all: 0.21 / Χ2: 0.981 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.955.20.8484190.4270.3950.940.86496.5
2.95-35.50.8574360.4740.3890.9460.88699.1
3-3.066.40.7744390.6470.3240.8420.87598.9
3.06-3.126.80.6974430.7820.2830.7540.87599.6
3.12-3.197.60.7524490.7660.290.8080.941100
3.19-3.278.60.6954260.8330.2490.7390.908100
3.27-3.358.90.5954500.8590.2080.6320.957100
3.35-3.4490.5364520.8860.1850.5680.951100
3.44-3.5490.4154440.9310.1440.441.077100
3.54-3.6590.3754430.9410.1310.3971.006100
3.65-3.788.90.314480.9550.1090.3291.054100
3.78-3.948.70.2644570.9680.0950.2811.084100
3.94-4.118.20.2174490.9690.080.2321.108100
4.11-4.338.70.1844460.9850.0660.1961.113100
4.33-4.69.20.164600.9890.0550.1691.024100
4.6-4.9690.1494500.9860.0520.1591.04100
4.96-5.458.80.1424710.9890.0510.1511.002100
5.45-6.247.80.1294660.990.0480.1380.967100
6.24-7.858.60.1024830.9950.0360.1090.892100
7.85-407.60.0685130.9960.0260.0730.82100

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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: 2.89→33.668 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.22
RfactorNum. reflection% reflection
Rfree0.2611 392 4.65 %
Rwork0.206 --
obs0.2084 8432 93.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 180.96 Å2 / Biso mean: 52.4257 Å2 / Biso min: 18.38 Å2
Refinement stepCycle: final / Resolution: 2.89→33.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 45 0 3492
Biso mean--48.58 --
Num. residues----447
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8901-3.3080.34591180.2986225480
3.308-4.16650.26091420.20992823100
4.1665-33.6680.22771320.1756296399
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)
13.0080.79690.26065.27821.36463.7484-0.2013-0.0941-0.2925-0.18950.0277-0.38650.414-0.03390.0910.2241-0.00440.06080.2613-0.00340.20699.603-27.554-15.347
21.06770.9347-1.20661.7011-0.74591.51650.23740.90940.3025-0.1801-0.7150.4911-0.1085-0.1979-0.20830.31720.0305-0.01050.4809-0.02160.45211.261-19.101-9.074
32.25991.6984-0.48943.6196-1.89041.73630.1306-0.59420.27710.6785-0.15240.305-0.1549-0.09140.02940.28380.02190.01820.369-0.06390.310812.901-10.753-7.728
42.08430.2235-1.1151.7705-1.64393.1127-0.16440.10681.00330.30140.24010.8632-0.526-0.5384-0.05580.29810.01410.06050.291-0.13580.621412.2013.394-13.734
50.67420.2063-0.07362.07450.24252.14550.00260.0426-0.10590.026-0.12530.13920.0756-0.23180.13660.15310.0393-0.00470.23910.01180.250520.024-15.408-24.246
61.46980.06130.68073.2983-0.47474.1348-0.0250.24880.1625-0.3915-0.06180.32120.0713-0.2180.08510.268-0.0343-0.02940.2790.02690.318412.375-10.145-37.503
71.7165-0.7124-0.0241.6987-0.0161.9213-0.21110.19360.40580.1658-0.5577-0.6666-0.17310.84750.24360.1162-0.02040.040.39260.02770.417127.543-14.835-25.885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:78 )A12 - 78
2X-RAY DIFFRACTION2( CHAIN A AND RESID 79:117 )A79 - 117
3X-RAY DIFFRACTION3( CHAIN A AND RESID 118:161 )A118 - 161
4X-RAY DIFFRACTION4( CHAIN A AND RESID 162:212 )A162 - 212
5X-RAY DIFFRACTION5( CHAIN A AND RESID 213:289 )A213 - 289
6X-RAY DIFFRACTION6( CHAIN A AND RESID 290:419 )A290 - 419
7X-RAY DIFFRACTION7( CHAIN A AND RESID 420:469 )A420 - 469

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