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- PDB-6l7h: crystal structure of GgCGT in complex with UDP and Nothofagin -

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Basic information

Entry
Database: PDB / ID: 6l7h
Titlecrystal structure of GgCGT in complex with UDP and Nothofagin
ComponentsGgCGT1
KeywordsTRANSFERASE / di-C-glycosyltransferase
Function / homologyChem-E7F / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesGlycyrrhiza glabra (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionNov 1, 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: GgCGT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3384
Polymers52,0931
Non-polymers1,2453
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-10 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.193, 71.306, 110.022
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 GgCGT1


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 / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-E7F / 1-[3-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-2,4,6-tris(oxidanyl)phenyl]-3-(4-hydroxyphenyl)propan-1-one / Nothofagin


Mass: 436.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24O10
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M BIS-Tris, pH 6.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.8→59.838 Å / Num. all: 39867 / Num. obs: 39867 / % possible obs: 99 % / Redundancy: 6.4 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.107 / Rsym value: 0.098 / Net I/av σ(I): 6.8 / Net I/σ(I): 12.5 / Num. measured all: 256181
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.94.60.6211.22631657500.3220.7030.6212.199.3
1.9-2.0150.4741.52753654770.2390.5330.4743.399.8
2.01-2.155.40.2872.62806151760.1370.3190.2875.3100
2.15-2.325.80.2053.52811948130.0930.2260.205899.9
2.32-2.556.30.14652829744680.0630.1590.14610.6100
2.55-2.8570.1076.62855140610.0430.1160.10714.1100
2.85-3.297.90.0729.72830735900.0270.0780.07220.5100
3.29-4.0290.05211.92758230700.0180.0550.05231.8100
4.02-5.6910.50.04413.42561824330.0140.0460.04439.8100
5.69-9.0027.60.05710.2779410290.0220.0610.05728.574.4

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L5P

6l5p


Resolution: 1.8→9.002 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.06
RfactorNum. reflection% reflection
Rfree0.2193 1973 4.96 %
Rwork0.1692 --
obs0.1717 39795 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.56 Å2 / Biso mean: 19.5475 Å2 / Biso min: 3.53 Å2
Refinement stepCycle: final / Resolution: 1.8→9.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 77 559 4144
Biso mean--13.87 29.18 -
Num. residues----453
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84470.27991280.21762614274299
1.8447-1.89410.25191210.209526982819100
1.8941-1.94930.28941390.226726782817100
1.9493-2.01150.27481210.21252657277899
2.0115-2.08260.25211480.189626972845100
2.0826-2.16480.23261430.177226642807100
2.1648-2.26190.23491510.170626682819100
2.2619-2.3790.23461480.17426812829100
2.379-2.5250.20681520.168526752827100
2.525-2.7150.21651520.170527122864100
2.715-2.97920.24821480.17127172865100
2.9792-3.390.18651380.16227442882100
3.39-4.19760.17861520.136427542906100
4.1976-9.0020.19661320.146828632995100

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