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- PDB-7msp: SunS glycosin S-glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7msp
TitleSunS glycosin S-glycosyltransferase
ComponentsSPbeta prophage-derived glycosyltransferase SunS
KeywordsBIOSYNTHETIC PROTEIN / glycosin / RiPP / S-glycosyltransferase
Function / homology
Function and homology information


: / bacteriocin biosynthetic process / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity
Similarity search - Function
Peptide S-glycosyltransferase, SunS family / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / SPbeta prophage-derived glycosyltransferase SunS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGarg, N. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079038 United States
CitationJournal: Cell Chem Biol / Year: 2021
Title: Structural and mechanistic investigations of protein S-glycosyltransferases.
Authors: Fujinami, D. / Garcia de Gonzalo, C.V. / Biswas, S. / Hao, Y. / Wang, H. / Garg, N. / Lukk, T. / Nair, S.K. / van der Donk, W.A.
History
DepositionMay 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPbeta prophage-derived glycosyltransferase SunS
B: SPbeta prophage-derived glycosyltransferase SunS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5146
Polymers79,3322
Non-polymers1,1814
Water5,314295
1
A: SPbeta prophage-derived glycosyltransferase SunS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2573
Polymers39,6661
Non-polymers5912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SPbeta prophage-derived glycosyltransferase SunS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2573
Polymers39,6661
Non-polymers5912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.850, 101.920, 135.830
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 SPbeta prophage-derived glycosyltransferase SunS


Mass: 39666.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sunS, yolJ, BSU21450 / Production host: Escherichia coli (E. coli)
References: UniProt: O31986, Transferases; Glycosyltransferases; Hexosyltransferases
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: PEG 4000 50 mM HEPES pH=7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48463 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 22.6
Reflection shellResolution: 2.1→2.2 Å / Num. unique obs: 1160 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→35.89 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2563 2422 5 %
Rwork0.2054 46027 -
obs0.2079 48449 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.44 Å2 / Biso mean: 48.4159 Å2 / Biso min: 22.17 Å2
Refinement stepCycle: final / Resolution: 2.1→35.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5550 0 74 295 5919
Biso mean--40.79 47.13 -
Num. residues----666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.140.32841400.286226452785
2.14-2.190.29171410.259426832824
2.19-2.240.26731380.231526192757
2.24-2.30.3071420.236927012843
2.3-2.360.25991420.238426962838
2.36-2.430.28471410.22126872828
2.43-2.510.27081400.220826422782
2.51-2.60.28431410.218526872828
2.6-2.70.24381420.214226942836
2.7-2.820.27081420.222726932835
2.82-2.970.27161410.226826842825
2.97-3.160.30221430.234927172860
3.16-3.40.2631430.22427272870
3.4-3.740.28011430.214227102853
3.74-4.280.24151450.178427562901
4.28-5.390.19551470.170827842931
5.39-35.890.24171510.17829023053

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