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- PDB-7vfm: Crystal structure of SdgB (UDP and SD peptide-binding form) -

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Basic information

Entry
Database: PDB / ID: 7vfm
TitleCrystal structure of SdgB (UDP and SD peptide-binding form)
Components
  • Glycosyl transferase, group 1 family protein
  • SER-ASP-SER-ASP
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
URIDINE-5'-DIPHOSPHATE / Glycosyl transferase, group 1 family protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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: 7EC4
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl transferase, group 1 family protein
C: Glycosyl transferase, group 1 family protein
E: SER-ASP-SER-ASP
G: SER-ASP-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1786
Polymers120,3704
Non-polymers8082
Water30617
1
A: Glycosyl transferase, group 1 family protein
E: SER-ASP-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5893
Polymers60,1852
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycosyl transferase, group 1 family protein
G: SER-ASP-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5893
Polymers60,1852
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.660, 206.662, 65.935
Angle α, β, γ (deg.)90.000, 104.830, 90.000
Int Tables number4
Space group name H-MP1211

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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: Protein/peptide SER-ASP-SER-ASP


Mass: 537.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
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 quick-soaked with 6.14 mM UDP and 2.45 mM 5-mer SD-repeat peptide (DSDSD)

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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: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 49800 / % possible obs: 99.6 % / Redundancy: 4.6 % / CC1/2: 0.995 / Net I/σ(I): 27.5
Reflection shellResolution: 2.28→2.32 Å / Num. unique obs: 2418 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EC1

7ec1


Resolution: 2.28→29.85 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2737 2653 5.34 %
Rwork0.2129 47048 -
obs0.2162 49701 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.78 Å2 / Biso mean: 50.3535 Å2 / Biso min: 18.85 Å2
Refinement stepCycle: final / Resolution: 2.28→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8220 0 65 17 8302
Biso mean--78.41 36.41 -
Num. residues----985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.28-2.320.3781210.31952258237992
2.32-2.370.39041400.294725702710100
2.37-2.410.34791300.285424302560100
2.41-2.470.36331500.275824792629100
2.47-2.520.36031520.257225062658100
2.52-2.590.26911300.242924432573100
2.59-2.660.37631250.244925662691100
2.66-2.740.34391380.256424692607100
2.74-2.820.34511460.263224902636100
2.82-2.920.38281370.252124662603100
2.92-3.040.33081480.252725192667100
3.04-3.180.3381380.239724532591100
3.18-3.350.30211340.241325192653100
3.35-3.560.28231270.210425162643100
3.56-3.830.23931420.200724852627100
3.83-4.210.25741600.184624532613100
4.21-4.820.20471240.16292501262599
4.82-6.070.21311650.183824912656100
6.07-29.850.22591460.18322434258097

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