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- PDB-7vfo: Crystal structure of SdgB (Phosphate-binding form) -

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Basic information

Entry
Database: PDB / ID: 7vfo
TitleCrystal structure of SdgB (Phosphate-binding 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
PHOSPHATE ION / Glycosyl transferase, group 1 family protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
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
Revision 1.2Oct 30, 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
B: Glycosyl transferase, group 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,82213
Polymers119,7772
Non-polymers1,04511
Water724
1
B: Glycosyl transferase, group 1 family protein
hetero molecules

A: Glycosyl transferase, group 1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,82213
Polymers119,7772
Non-polymers1,04511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x+y-1,-x,z-2/31
Buried area4640 Å2
ΔGint-62 kcal/mol
Surface area43250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.257, 172.257, 106.174
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glycosyl transferase, group 1 family protein


Mass: 59888.504 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 1.2 M NaH2PO4, 0.8 M K2HPO4, and 0.1 M CAPS-NaOH (pH 10.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26949 / % possible obs: 89 % / Redundancy: 8.2 % / CC1/2: 0.973 / Net I/σ(I): 16.9
Reflection shellResolution: 3.2→3.26 Å / Num. unique obs: 1492 / CC1/2: 0.916

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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: 3.2→29.98 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 1357 5.04 %
Rwork0.197 25542 -
obs0.2003 26899 88.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.2 Å2 / Biso mean: 55.4195 Å2 / Biso min: 24.33 Å2
Refinement stepCycle: final / Resolution: 3.2→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8254 0 55 4 8313
Biso mean--82.6 44.78 -
Num. residues----990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.310.31721680.23692825299399
3.31-3.450.32471470.22582809295699
3.45-3.60.28941410.22212780292198
3.6-3.790.28441440.20012713285796
3.79-4.030.26811470.18892594274191
4.03-4.340.2151220.18382459258186
4.34-4.780.24241300.16872388251884
4.78-5.460.27391170.18342373249082
5.46-6.870.26121250.21412343246881
6.87-29.980.21191160.18752258237475

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