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- PDB-6l5s: crystal structure of GgCGT in complex with UDP-Glu -

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Basic information

Entry
Database: PDB / ID: 6l5s
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: 1.914 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

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Assembly

Deposited unit
A: GgCGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9565
Polymers52,0931
Non-polymers8634
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-9 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.376, 70.620, 108.402
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 426 / 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: 1.96 Å3/Da / Density % sol: 37.28 %
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: 1.9→40 Å / Num. obs: 31904 / % possible obs: 99.5 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.056 / Rrim(I) all: 0.176 / Χ2: 0.984 / Net I/σ(I): 3.9 / Num. measured all: 293646
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.938.80.77315450.7790.2690.820.883100
1.93-1.979.10.72215860.7980.2480.7660.898100
1.97-2.019.20.63815850.8420.2190.6770.94499.9
2.01-2.059.10.57115510.8560.1960.6050.955100
2.05-2.0990.5215810.8840.1790.5510.99199.9
2.09-2.148.40.44415870.9140.1590.4731.02199.9
2.14-2.198.90.4115870.9170.1430.4361.036100
2.19-2.259.70.37215710.940.1230.3931.08799.9
2.25-2.329.60.34415630.9450.1150.3641.07599.9
2.32-2.399.60.30516230.9570.1020.3221.073100
2.39-2.489.50.26915780.9630.090.2851.12199.8
2.48-2.589.50.24115850.9710.0810.2551.11499.7
2.58-2.790.21415800.9740.0730.2271.12499.4
2.7-2.848.50.18716040.9810.0660.1981.12999.9
2.84-3.029.90.15716010.9870.0510.1661.08699.7
3.02-3.259.70.13316070.990.0430.141.03799.7
3.25-3.589.50.10516090.9930.0350.1110.96799.3
3.58-4.098.60.08716100.9960.030.0920.86398.5
4.09-5.159.50.07316520.9970.0240.0770.70398.8
5.15-408.90.06616990.9980.0220.070.58196.6

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Processing

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

2acw


Resolution: 1.914→33.484 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1599 5.04 %
Rwork0.1579 30146 -
obs0.1604 31745 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.53 Å2 / Biso mean: 24.7488 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: final / Resolution: 1.914→33.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 57 426 4003
Biso mean--25.39 32.46 -
Num. residues----454
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9141-1.97580.25671110.2027246789
1.9758-2.04650.22681480.19072725100
2.0465-2.12840.23791410.17782732100
2.1284-2.22520.24311190.1688276999
2.2252-2.34250.23251590.16782725100
2.3425-2.48920.22171670.16642733100
2.4892-2.68140.23371530.1671277099
2.6814-2.9510.20051460.16552787100
2.951-3.37770.21891530.1552792100
3.3777-4.25420.18131410.1343279499
4.2542-33.4840.16881610.1437285296
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)
11.18120.33420.06631.01230.21730.9148-0.0066-0.06540.04370.10370.002-0.1304-0.04630.1016-0.01080.1430.0076-0.01770.1253-0.00720.110345.17854.39741.944
20.86040.42990.2581.83912.01283.0075-0.0243-0.025-0.11850.39960.2346-0.38460.19620.8984-0.19940.23380.0311-0.07750.30960.02180.220645.0336.55539.152
30.85450.032-0.01760.81310.01581.3319-0.00450.05520.0591-0.0676-0.00150.023-0.05420.00910.00310.0953-0.0006-0.00570.07730.01020.099336.60350.85921.62
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:181 )A6 - 181
2X-RAY DIFFRACTION2( CHAIN A AND RESID 182:212 )A182 - 212
3X-RAY DIFFRACTION3( CHAIN A AND RESID 213:469 )A213 - 469

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