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- PDB-8ila: Crystal structure of LmbT from Streptomyces lincolnensis NRRL ISP... -

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Basic information

Entry
Database: PDB / ID: 8ila
TitleCrystal structure of LmbT from Streptomyces lincolnensis NRRL ISP-5355 in complex with substrates
ComponentsGlycosyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Glycosyltransferase
Function / homologyGlycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / GUANOSINE-5'-DIPHOSPHATE / Chem-Q3L / LmbT
Function and homology information
Biological speciesStreptomyces lincolnensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsDai, Y. / Qiao, H. / Xia, M. / Fang, P. / Liu, W.
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 3, 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
A: Glycosyltransferase
C: Glycosyltransferase
B: Glycosyltransferase
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,15012
Polymers197,6354
Non-polymers3,5158
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-43 kcal/mol
Surface area60220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.382, 137.739, 146.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glycosyltransferase


Mass: 49408.723 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-Q3L / (2~{S})-3-[2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-[(1~{R},2~{R})-1-azanyl-2-oxidanyl-propyl]-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanyl-1~{H}-imidazol-5-yl]-2-(trimethyl-$l^{4}-azanyl)propanoic acid


Mass: 435.516 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H31N4O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 8% PEG 20000, 0.05 M Tris pH 8.5, 1.2 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.79→100.22 Å / Num. obs: 62181 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.2
Reflection shellResolution: 2.79→2.94 Å / Num. unique obs: 9020 / CC1/2: 0.828 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→68.87 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 3095 5 %
Rwork0.2379 --
obs0.24 61919 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→68.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13221 0 0 57 13278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.184
X-RAY DIFFRACTIONf_dihedral_angle_d18.1425004
X-RAY DIFFRACTIONf_chiral_restr0.0632024
X-RAY DIFFRACTIONf_plane_restr0.0112433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.830.33391390.34822668X-RAY DIFFRACTION100
2.83-2.880.42571360.32732664X-RAY DIFFRACTION100
2.88-2.930.36851460.31592658X-RAY DIFFRACTION100
2.93-2.980.31031100.29782683X-RAY DIFFRACTION100
2.98-3.040.29221430.29042631X-RAY DIFFRACTION100
3.04-3.10.37631280.29452689X-RAY DIFFRACTION100
3.1-3.170.36221280.29572667X-RAY DIFFRACTION100
3.17-3.240.33121250.31262705X-RAY DIFFRACTION100
3.24-3.320.3511520.32252640X-RAY DIFFRACTION100
3.32-3.410.34751610.29872658X-RAY DIFFRACTION100
3.41-3.510.40881350.30942547X-RAY DIFFRACTION96
3.51-3.620.26321240.24882703X-RAY DIFFRACTION100
3.62-3.750.33511350.28372571X-RAY DIFFRACTION96
3.75-3.90.33161300.2722611X-RAY DIFFRACTION97
3.9-4.080.26721280.23522640X-RAY DIFFRACTION97
4.08-4.30.23871290.20192702X-RAY DIFFRACTION100
4.3-4.570.22921410.19052697X-RAY DIFFRACTION100
4.57-4.920.251470.20142700X-RAY DIFFRACTION100
4.92-5.410.24831760.21232690X-RAY DIFFRACTION100
5.41-6.190.27351670.21372713X-RAY DIFFRACTION100
6.2-7.80.241530.20882753X-RAY DIFFRACTION100
7.8-68.870.21311620.17692834X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 39.3314 Å / Origin y: 20.9171 Å / Origin z: 31.341 Å
111213212223313233
T0.58 Å2-0.0372 Å20.0024 Å2-0.5675 Å20.0606 Å2--0.5726 Å2
L0.4338 °2-0.1076 °2-0.021 °2-0.3606 °2-0.0572 °2--0.3631 °2
S-0 Å °-0.0662 Å °-0.0756 Å °0.0701 Å °0.0372 Å °0.0727 Å °0.0597 Å °-0.0659 Å °-0.0424 Å °
Refinement TLS groupSelection details: all

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