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- PDB-8il0: Crystal structure of LmbT from Streptomyces lincolnensis NRRL ISP-5355 -

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Basic information

Entry
Database: PDB / ID: 8il0
TitleCrystal structure of LmbT from Streptomyces lincolnensis NRRL ISP-5355
ComponentsGlycosyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Glycosyltransferase
Function / homologyGlycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / D-inositol 3-phosphate glycosyltransferase
Function and homology information
Biological speciesStreptomyces lincolnensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsDai, Y. / Li, P. / Qiao, H. / Xia, M. / Liu, W. / Fang, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22277132 China
National Natural Science Foundation of China (NSFC)21977107 China
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Structural Basis of Low-Molecular-Weight Thiol Glycosylation in Lincomycin A Biosynthesis.
Authors: Dai, Y. / Cheng, Y. / Ding, W. / Qiao, H. / Zhang, D. / Zhong, G. / Xia, M. / Tao, J. / Sun, P. / Fang, P. / Liu, W.
History
DepositionMar 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)49,4091
Polymers49,4091
Non-polymers00
Water00
1
F: Glycosyltransferase

F: Glycosyltransferase

F: Glycosyltransferase

F: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)197,6354
Polymers197,6354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area9180 Å2
ΔGint-19 kcal/mol
Surface area63930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.741, 103.741, 197.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Glycosyltransferase


Mass: 49408.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lincolnensis (bacteria) / Gene: GJU35_01490 / Production host: Escherichia coli (E. coli) / References: UniProt: A9Y8T1

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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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium acetate tetrahydrate, 0.1 M MES, pH6.5 10 %, w/v PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979021 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979021 Å / Relative weight: 1
ReflectionResolution: 2.81→91.82 Å / Num. obs: 12924 / % possible obs: 95.3 % / Redundancy: 10 % / CC1/2: 0.999 / Net I/σ(I): 23
Reflection shellResolution: 2.81→2.96 Å / Num. unique obs: 1925 / CC1/2: 0.831

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→49.31 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 657 5.09 %
Rwork0.2314 --
obs0.2328 12903 95.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 0 0 3248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.242
X-RAY DIFFRACTIONf_dihedral_angle_d17.1571200
X-RAY DIFFRACTIONf_chiral_restr0.067499
X-RAY DIFFRACTIONf_plane_restr0.008606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-3.030.42491340.3672509X-RAY DIFFRACTION100
3.03-3.330.36641400.31162529X-RAY DIFFRACTION100
3.33-3.810.33711100.29272120X-RAY DIFFRACTION84
3.81-4.80.22861340.21472380X-RAY DIFFRACTION93
4.8-49.310.21631390.1972708X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.9425 Å / Origin y: -2.6882 Å / Origin z: 19.8275 Å
111213212223313233
T0.8457 Å2-0.1014 Å2-0.1408 Å2-0.7105 Å20.03 Å2--0.7892 Å2
L0.4985 °2-0.313 °20.0143 °2-0.518 °2-0.4248 °2--0.7917 °2
S-0.189 Å °-0.0026 Å °0.1733 Å °0.2344 Å °0.0864 Å °-0.2018 Å °-0.1503 Å °0.1021 Å °0.0951 Å °
Refinement TLS groupSelection details: all

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