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- PDB-6lfn: Crystal structure of LpCGTb -

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Basic information

Entry
Database: PDB / ID: 6lfn
TitleCrystal structure of LpCGTb
ComponentsLpCGTb
KeywordsTRANSFERASE / LpCGTb protein
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesLandoltia punctata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.395 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 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: LpCGTb
B: LpCGTb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1724
Polymers100,9822
Non-polymers1902
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-15 kcal/mol
Surface area34900 Å2
Unit cell
Length a, b, c (Å)78.343, 87.821, 134.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein LpCGTb


Mass: 50491.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Landoltia punctata (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate monohydrate, 0.1M 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: 0.97851 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: 2.395→33.603 Å / Num. obs: 36830 / % possible obs: 99.02 % / Redundancy: 6.3 % / Biso Wilson estimate: 45.67 Å2 / Rpim(I) all: 0.052 / Net I/σ(I): 14.8
Reflection shellResolution: 2.395→2.44 Å / Num. unique obs: 3211 / Rpim(I) all: 0.376

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LF6

6lf6


Resolution: 2.395→33.603 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 1764 4.79 %
Rwork0.2109 35066 -
obs0.2131 36830 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.98 Å2 / Biso mean: 51.3329 Å2 / Biso min: 20.22 Å2
Refinement stepCycle: final / Resolution: 2.395→33.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 10 0 6544
Biso mean--56.91 --
Num. residues----883
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3953-2.460.33831140.2881257095
2.46-2.53240.35681390.2907265099
2.5324-2.61410.32491370.2696266199
2.6141-2.70750.32451430.2668267199
2.7075-2.81580.2931280.2756264299
2.8158-2.94390.31421280.2789268699
2.9439-3.0990.28131370.2594268499
3.099-3.2930.3411470.24162683100
3.293-3.5470.26731260.21942725100
3.547-3.90350.22851450.19232706100
3.9035-4.46720.21921370.1652750100
4.4672-5.6240.18411280.17432786100
5.624-33.6030.2371550.1818285298

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