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- PDB-7ec1: Crystal structure of SdgB (ligand-free form) -

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Basic information

Entry
Database: PDB / ID: 7ec1
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: 1.85 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 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 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)120,08910
Polymers119,2952
Non-polymers7958
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint3 kcal/mol
Surface area44150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.968, 206.342, 66.329
Angle α, β, γ (deg.)90.000, 105.070, 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.38 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: 1.85→30 Å / Num. obs: 93867 / % possible obs: 98.4 % / Redundancy: 3.8 % / CC1/2: 0.996 / Net I/σ(I): 26.3
Reflection shellResolution: 1.85→1.88 Å / Num. unique obs: 4772 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.945 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4712 5 %RANDOM
Rwork0.2081 ---
obs0.2103 89189 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.67 Å2 / Biso mean: 38.816 Å2 / Biso min: 15.88 Å2
Baniso -1Baniso -2Baniso -3
1-3.79 Å20 Å20.99 Å2
2---3.53 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 1.85→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8346 0 52 387 8785
Biso mean--50.85 40.79 -
Num. residues----1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138605
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177977
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.64211629
X-RAY DIFFRACTIONr_angle_other_deg1.2761.57918346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1595997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59922.871505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03151491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4711546
X-RAY DIFFRACTIONr_chiral_restr0.0710.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022134
LS refinement shellResolution: 1.841→1.889 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 355 -
Rwork0.313 6205 -
all-6560 -
obs--92.88 %

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