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- PDB-6lfz: Crystal structure of SbCGTb in complex with UDPG -

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Basic information

Entry
Database: PDB / ID: 6lfz
TitleCrystal structure of SbCGTb in complex with UDPG
ComponentsSbCGTb
KeywordsTRANSFERASE
Function / homologyURIDINE-5'-DIPHOSPHATE-GLUCOSE
Function and homology information
Biological speciesScutellaria baicalensis (Baikal skullcap)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.866 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

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Assembly

Deposited unit
A: SbCGTb
B: SbCGTb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1134
Polymers102,9802
Non-polymers1,1332
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-16 kcal/mol
Surface area34420 Å2
Unit cell
Length a, b, c (Å)107.287, 216.953, 104.705
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 SbCGTb


Mass: 51489.992 Da / Num. of mol.: 2
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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.05 M calcium chloride,0.05 M barium chloride,0.1 M Tris,32 % v/v PEG 400, 0.01 M GSH (L-Glutathione reduced), 0.01 M GSSG (L Glutathione oxidized)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.866→36.159 Å / Num. obs: 28244 / % possible obs: 99.29 % / Redundancy: 12.1 % / Biso Wilson estimate: 44.21 Å2 / Rpim(I) all: 0.089 / Net I/σ(I): 4.4
Reflection shellResolution: 2.866→2.95 Å / Num. unique obs: 3473 / Rpim(I) all: 0.661 / % possible all: 84.7

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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: 6L5P

6l5p


Resolution: 2.866→36.159 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1337 4.73 %
Rwork0.2176 26907 -
obs0.2193 28244 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.55 Å2 / Biso mean: 40.3625 Å2 / Biso min: 14.66 Å2
Refinement stepCycle: final / Resolution: 2.866→36.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 72 53 6852
Biso mean--56.88 38.42 -
Num. residues----874
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8662-2.96860.31861240.2758255596
2.9686-3.08740.29391210.26722676100
3.0874-3.22780.32541440.25272667100
3.2278-3.39790.26531380.24382693100
3.3979-3.61060.23781240.22412694100
3.6106-3.8890.24721340.19822699100
3.889-4.27980.23441130.19232705100
4.2798-4.89780.21131610.18262700100
4.8978-6.16580.27051390.22092741100
6.1658-36.1590.24931390.216277797

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