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- PDB-7ec3: Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycos... -

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Basic information

Entry
Database: PDB / ID: 7ec3
TitleCrystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide)
Components
  • 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
  • Glycosyl transferase, group 1 family protein
KeywordsTRANSFERASE / Glycosylation
Function / homologyGlycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / cytoplasm / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase, group 1 family protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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)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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
D: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
G: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,83011
Polymers120,9164
Non-polymers1,9147
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint6 kcal/mol
Surface area44090 Å2
Unit cell
Length a, b, c (Å)70.201, 130.568, 189.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl transferase, group 1 family protein


Mass: 59631.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / Gene: SAUSA300_0550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2XGN0
#2: Protein/peptide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-35)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-65)]5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE


Mass: 826.678 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 / Comment: UDP*YM
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 20 mM CaCl2, 85 mM tri-sodium citrate at pH 5.6, 25.5% (w/v) PEG 4,000, and 15% (w/v) glycerol for the SdgB crystal soaked with the 2.66 mM 9mer SD-repeat peptide and 9.60 mM UDP-GlcNAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 60708 / % possible obs: 96.7 % / Redundancy: 5.4 % / CC1/2: 0.934 / Net I/σ(I): 12.9
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2941 / 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: 2.5→47.05 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.08 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3041 5 %RANDOM
Rwork0.191 ---
obs0.193 57606 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.14 Å2 / Biso mean: 38.96 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--4.83 Å20 Å2
3----3.06 Å2
Refinement stepCycle: final / Resolution: 2.5→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8433 0 122 24 8579
Biso mean--37 30.01 -
Num. residues----1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177974
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.67911885
X-RAY DIFFRACTIONr_angle_other_deg1.2471.58818344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4175998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76722.908502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.141151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8261546
X-RAY DIFFRACTIONr_chiral_restr0.080.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022136
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

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