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- PDB-7msk: ThuS glycosin S-glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7msk
TitleThuS glycosin S-glycosyltransferase
ComponentsGlyco_trans_2-like domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / glycosin / RiPP / glycosyltransferase
Function / homology: / Peptide S-glycosyltransferase, SunS family / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / Chem-U2F / Glyco_trans_2-like domain-containing protein
Function and homology information
Biological speciesBacillus thuringiensis serovar andalousiensis BGSC 4AW1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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: Glyco_trans_2-like domain-containing protein
B: Glyco_trans_2-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0946
Polymers100,9092
Non-polymers1,1854
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-63 kcal/mol
Surface area39070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.833, 112.654, 90.310
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glyco_trans_2-like domain-containing protein


Mass: 50454.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar andalousiensis BGSC 4AW1 (bacteria)
Gene: bthur0009_56280 / Production host: Escherichia coli (E. coli) / References: UniProt: C3GCL5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23FN2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 3350 200 mM ammonium nitrate 100 mM BisTris HCl pH=6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.06→90.3 Å / Num. obs: 61544 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 16.9
Reflection shellResolution: 2.06→2.09 Å / Num. unique obs: 3042 / CC1/2: 0.831

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.602 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 3066 5 %RANDOM
Rwork0.2005 ---
obs0.2024 58262 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.68 Å2 / Biso mean: 41.5 Å2 / Biso min: 19.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.74 Å2
2--2.58 Å2-0 Å2
3----2.64 Å2
Refinement stepCycle: final / Resolution: 2.06→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6954 0 74 337 7365
Biso mean--32.34 42.68 -
Num. residues----842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127190
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176965
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.6359739
X-RAY DIFFRACTIONr_angle_other_deg0.3961.5815856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24923.453391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.425151338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2541536
X-RAY DIFFRACTIONr_chiral_restr0.0560.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021644
LS refinement shellResolution: 2.06→2.113 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 196 -
Rwork0.288 4233 -
all-4429 -
obs--99.37 %

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