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- PDB-7vfk: Crystal structure of SdgB (ligand-free form) -

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Basic information

Entry
Database: PDB / ID: 7vfk
TitleCrystal structure of SdgB (ligand-free form)
ComponentsGlycosyl transferase, group 1 family protein
KeywordsTRANSFERASE / Glycosylation
Function / homology
Function and homology information


glycosyltransferase activity / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Glycosyl transferase, group 1 family protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsKim, D.-G. / Baek, I. / Lee, Y. / Kim, H.S.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1C1C1009512 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017R1C1B2012225 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2015R1D1A4A01020265 Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins.
Authors: Kim, D.G. / Baek, I. / Lee, Y. / Kim, H. / Kim, J.Y. / Bang, G. / Kim, S. / Yoon, H.J. / Han, B.W. / Suh, S.W. / Kim, H.S.
History
DepositionSep 13, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 24, 2021ID: 7EC2
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 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: Glycosyl transferase, group 1 family protein
B: Glycosyl transferase, group 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9058
Polymers119,2952
Non-polymers6116
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-5 kcal/mol
Surface area43820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.968, 206.342, 66.329
Angle α, β, γ (deg.)90.000, 105.065, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycosyl transferase, group 1 family protein


Mass: 59647.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Strain: USA300 / Gene: SAUSA300_0550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2XGN0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M Tris-HCl (pH 8.5), and 25% (w/v) polyethylene glycol (PEG) 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 93892 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.32 Å2 / CC1/2: 0.996 / Net I/σ(I): 26.3
Reflection shellResolution: 1.84→1.88 Å / Num. unique obs: 4772 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→29.26 Å / SU ML: 0.2655 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.6704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2585 4712 5.02 %
Rwork0.2168 89180 -
obs0.2189 93892 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.23 Å2
Refinement stepCycle: LAST / Resolution: 1.84→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8263 0 40 378 8681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828506
X-RAY DIFFRACTIONf_angle_d0.954311493
X-RAY DIFFRACTIONf_chiral_restr0.05861222
X-RAY DIFFRACTIONf_plane_restr0.00721467
X-RAY DIFFRACTIONf_dihedral_angle_d7.28591117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.33841460.31542577X-RAY DIFFRACTION84.91
1.86-1.880.32121670.29492985X-RAY DIFFRACTION99.75
1.88-1.910.33551710.29322969X-RAY DIFFRACTION99.84
1.91-1.930.30891650.2913030X-RAY DIFFRACTION99.38
1.93-1.960.33711270.29113095X-RAY DIFFRACTION99.2
1.96-1.980.30311600.28242942X-RAY DIFFRACTION99.71
1.98-2.010.34061660.28133018X-RAY DIFFRACTION99.34
2.01-2.040.32911570.27343057X-RAY DIFFRACTION98.86
2.04-2.070.34691610.27822973X-RAY DIFFRACTION99.59
2.07-2.110.36131490.27272969X-RAY DIFFRACTION99.02
2.11-2.140.32891850.27033051X-RAY DIFFRACTION98.6
2.14-2.180.29311530.25362940X-RAY DIFFRACTION99.26
2.18-2.230.26741570.24393010X-RAY DIFFRACTION98.85
2.23-2.270.26491570.24662991X-RAY DIFFRACTION98.1
2.27-2.320.29821420.24732958X-RAY DIFFRACTION98.95
2.32-2.370.27141750.2363038X-RAY DIFFRACTION98.29
2.37-2.430.281460.24262968X-RAY DIFFRACTION98.7
2.43-2.50.30141680.24312989X-RAY DIFFRACTION98.47
2.5-2.570.32481580.23782981X-RAY DIFFRACTION98.22
2.57-2.660.31500.23153011X-RAY DIFFRACTION98.32
2.66-2.750.32251590.22992946X-RAY DIFFRACTION98.04
2.75-2.860.26041450.23233016X-RAY DIFFRACTION97.71
2.86-2.990.28311490.22672967X-RAY DIFFRACTION98.89
2.99-3.150.29991540.21943005X-RAY DIFFRACTION97.92
3.15-3.340.26581650.22132953X-RAY DIFFRACTION97.74
3.34-3.60.26941590.20732971X-RAY DIFFRACTION98.12
3.6-3.960.22461630.18862970X-RAY DIFFRACTION98.15
3.96-4.540.21171380.172977X-RAY DIFFRACTION97.34
4.54-5.710.18411650.172991X-RAY DIFFRACTION98.23
5.71-29.260.18671550.18742832X-RAY DIFFRACTION91.88

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