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- PDB-7ec6: Crystal structure of SdgB (complexed with peptides) -

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Basic information

Entry
Database: PDB / ID: 7ec6
TitleCrystal structure of SdgB (complexed with peptides)
Components
  • ASP-SER-ASP
  • Glycosyl transferase, group 1 family protein
KeywordsTRANSFERASE / Glycosylation
Function / homologyGlycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / Glycogen Phosphorylase B; / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Glycosyl transferase, group 1 family protein
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase, group 1 family protein
C: Glycosyl transferase, group 1 family protein
D: ASP-SER-ASP


Theoretical massNumber of molelcules
Total (without water)119,6303
Polymers119,6303
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-3 kcal/mol
Surface area43930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.150, 206.172, 66.400
Angle α, β, γ (deg.)90.000, 105.320, 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 ASP-SER-ASP


Mass: 335.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
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 incubated with the 2.45 mM 3-mer SD-repeat peptide and 6.14 mM UDP-GlcNAc

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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: 1.9→30 Å / Num. obs: 87189 / % possible obs: 99.3 % / Redundancy: 4.1 % / CC1/2: 0.992 / Net I/σ(I): 26
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 4385 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EC1

7ec1


Resolution: 1.9→29.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.407 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 4391 5 %RANDOM
Rwork0.2294 ---
obs0.231 82563 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.48 Å2 / Biso mean: 38.075 Å2 / Biso min: 15.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å2-0.64 Å2
2--0.85 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.9→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8208 0 23 201 8432
Biso mean--50.55 35.05 -
Num. residues----984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138461
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177828
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.64511444
X-RAY DIFFRACTIONr_angle_other_deg1.2851.57917999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0255979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43622.86493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.564151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7631544
X-RAY DIFFRACTIONr_chiral_restr0.0710.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022100
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 326 -
Rwork0.377 6156 -
all-6482 -
obs--99.98 %

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