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- PDB-6l5p: crystal structure of GgCGT in complex with UDP-Glu -

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Basic information

Entry
Database: PDB / ID: 6l5p
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 / URIDINE-5'-DIPHOSPHATE-GLUCOSE
Function and homology information
Biological speciesGlycyrrhiza glabra (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 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
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.178, 139.468, 73.892
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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 13994 / % possible obs: 98.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.032 / Rrim(I) all: 0.08 / Χ2: 0.743 / Net I/σ(I): 5.5 / Num. measured all: 85426
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.646.30.9136940.8460.3920.9960.63997.5
2.64-2.696.30.7826820.8750.3360.8520.666100
2.69-2.746.20.7056860.9060.3040.7690.66197.6
2.74-2.86.20.5756770.9350.250.6290.679100
2.8-2.866.20.4816950.9310.2070.5250.72897.9
2.86-2.936.20.4176850.9560.180.4550.75298.3
2.93-36.20.3376860.9470.1460.3680.75798.3
3-3.086.10.2826890.9680.1240.3080.76698.4
3.08-3.175.80.2267020.9680.1030.2490.895100
3.17-3.285.90.1866810.9760.0820.2040.89898.7
3.28-3.395.90.1556780.9790.0690.170.91198.3
3.39-3.536.50.1467080.9840.0620.1590.88999.2
3.53-3.696.40.1197040.9860.050.1290.91799.4
3.69-3.886.40.1036940.9890.0440.1120.91899.6
3.88-4.136.20.0787130.9890.0340.0850.88799.3
4.13-4.445.90.0656990.990.0280.0710.81699.6
4.44-4.895.60.0567010.9950.0250.0620.76399.3
4.89-5.66.20.0497200.9920.0210.0530.57799.4
5.6-7.056.20.047320.9940.0170.0440.45299.5
7.05-405.40.0297680.9980.0130.0320.28798.1

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Processing

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

2acw


Resolution: 2.603→28.448 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 581 5.08 %
Rwork0.2367 10865 -
obs0.2387 11446 80.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.9 Å2 / Biso mean: 49.8755 Å2 / Biso min: 3.61 Å2
Refinement stepCycle: final / Resolution: 2.603→28.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 36 34 3423
Biso mean--24.65 26.98 -
Num. residues----436
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6034-2.86510.3609770.3013126539
2.8651-3.27920.31441530.2923283986
3.2792-4.12940.29561590.2455333299
4.1294-28.4480.23781920.201342999
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)
12.02390.1607-0.20710.6360.15881.62240.429-0.24220.02920.02550.1186-0.66190.0121.09350.552-0.34920.12160.29860.2829-0.0097-0.2036-16.291-9.324-10.804
20.9487-0.1948-0.19230.91911.41032.3369-0.1647-0.2657-0.81760.8941-0.07720.32571.51120.1081-0.41990.48270.1510.02980.07770.13560.4647-25.25-27.051-6.908
30.01240.05560.06290.27540.32230.3806-0.02630.2321-0.0558-0.47850.1158-0.4842-0.16120.58420.77060.2990.1310.38370.4459-0.00620.1523-8.387-11.01-26.008
43.0192-0.42650.46692.7816-0.60913.70240.42880.39510.1781-0.14350.07880.3358-0.77370.1223-0.25250.39640.08680.08640.45240.03110.1817-22.352-0.871-28.137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 346:469 )A346 - 469
2X-RAY DIFFRACTION2( CHAIN A AND RESID 16:251 )A16 - 251
3X-RAY DIFFRACTION3( CHAIN A AND RESID 252:281 )A252 - 281
4X-RAY DIFFRACTION4( CHAIN A AND RESID 282:345 )A282 - 345

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