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- PDB-6lg0: Crystal structure of SbCGTa in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 6lg0
TitleCrystal structure of SbCGTa in complex with UDP
ComponentsSbCGTa
KeywordsTRANSFERASE
Function / homologyGlycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesScutellaria baicalensis (Baikal skullcap)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.998 Å
AuthorsGao, H.M. / Yun, C.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Dissection of the general two-step di- C -glycosylation pathway for the biosynthesis of (iso)schaftosides in higher plants.
Authors: Wang, Z.L. / Gao, H.M. / Wang, S. / Zhang, M. / Chen, K. / Zhang, Y.Q. / Wang, H.D. / Han, B.Y. / Xu, L.L. / Song, T.Q. / Yun, C.H. / Qiao, X. / Ye, M.
History
DepositionDec 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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: SbCGTa
B: SbCGTa
C: SbCGTa
D: SbCGTa
E: SbCGTa
F: SbCGTa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,43112
Polymers303,0066
Non-polymers2,4256
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-83 kcal/mol
Surface area103150 Å2
Unit cell
Length a, b, c (Å)97.318, 171.593, 179.169
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
SbCGTa


Mass: 50500.926 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scutellaria baicalensis (Baikal skullcap)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium citrate tribasic pH7.0 20%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.998→46.958 Å / Num. obs: 59473 / % possible obs: 97.61 % / Redundancy: 6 % / Biso Wilson estimate: 57.33 Å2 / Rpim(I) all: 0.095 / Net I/σ(I): 7.65
Reflection shellResolution: 3→3.23 Å / Num. unique obs: 11419 / Rpim(I) all: 0.689

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LFZ

6lfz


Resolution: 2.998→46.958 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 2944 4.95 %
Rwork0.2421 56529 -
obs0.2436 59473 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.74 Å2 / Biso mean: 48.1958 Å2 / Biso min: 11.79 Å2
Refinement stepCycle: final / Resolution: 2.998→46.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19362 0 150 10 19522
Biso mean--49.49 36.98 -
Num. residues----2651
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.998-3.04670.38071210.3232240988
3.0467-3.09920.34071240.3109257795
3.0992-3.15550.33551370.2964257895
3.1555-3.21620.31511210.2831261996
3.2162-3.28190.29221260.2789264596
3.2819-3.35320.32771400.2873270398
3.3532-3.43120.32481420.2774268699
3.4312-3.5170.34221380.2775268898
3.517-3.6120.2751580.2705264297
3.612-3.71830.26911430.2371265897
3.7183-3.83820.23121230.2424271699
3.8382-3.97530.27361320.2276274899
3.9753-4.13440.29741650.22532706100
4.1344-4.32240.24511660.21472710100
4.3224-4.55020.24461390.21012757100
4.5502-4.8350.23821470.21752757100
4.835-5.20780.26111170.2257276699
5.2078-5.73110.27081730.2457271398
5.7311-6.55850.22991420.25792799100
6.5585-8.25570.26771500.23872826100
8.2557-46.9580.22791400.2053282695

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