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- PDB-6lg1: Crystal structure of LpCGTa in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 6lg1
TitleCrystal structure of LpCGTa in complex with UDP
ComponentsLpCGTa
KeywordsTRANSFERASE / LpCGTa / UDP / Complex
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesLandoltia punctata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.047 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: LpCGTa
B: LpCGTa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8764
Polymers103,0672
Non-polymers8082
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-26 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.447, 87.703, 201.328
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 LpCGTa


Mass: 51533.723 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) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / 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.: 1 / 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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.8M Potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5,0.5%(w/v) Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 28294 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 89.69 Å2 / Rpim(I) all: 0.049 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.23 Å / Num. unique obs: 5553 / Rpim(I) all: 0.563 / % possible all: 100

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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: 6LFN

6lfn


Resolution: 3.047→43.654 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 1272 4.74 %
Rwork0.2473 25588 -
obs0.2489 26860 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.06 Å2 / Biso mean: 77.1784 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.047→43.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5879 0 50 1 5930
Biso mean--68.7 30 -
Num. residues----854
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0471-3.1690.40131350.3524275198
3.169-3.31320.3491260.29722816100
3.3132-3.48780.32511410.28362826100
3.4878-3.70620.32291570.27292793100
3.7062-3.99220.31941320.2452836100
3.9922-4.39360.2571680.22482813100
4.3936-5.02860.2391370.22322846100
5.0286-6.33240.27291540.25992893100
6.3324-43.6540.26621220.228301498

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