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- PDB-8tb2: Structure of SasG (type II) (residues 165-421) from Staphylococcu... -

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Basic information

Entry
Database: PDB / ID: 8tb2
TitleStructure of SasG (type II) (residues 165-421) from Staphylococcus aureus MW2
ComponentsPutative surface protein MW2416
KeywordsCELL ADHESION / Lectin / SASG / adhesin
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Legume lectin beta-barrel domain / E domain / E domain / G5 domain / G5 domain / G5 domain profile. / G5 / : / YSIRK type signal peptide / YSIRK Gram-positive signal peptide ...Legume lectin beta-barrel domain / E domain / E domain / G5 domain / G5 domain / G5 domain profile. / G5 / : / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Putative surface protein MW2416
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus MW2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMaciag, J.J. / Herr, A.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM094363 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI162964 United States
CitationJournal: Cell Rep / Year: 2024
Title: Staphylococcus aureus skin colonization is mediated by SasG lectin variation.
Authors: Mills, K.B. / Maciag, J.J. / Wang, C. / Crawford, J.A. / Enroth, T.J. / Keim, K.C. / Dufrene, Y.F. / Robinson, D.A. / Fey, P.D. / Herr, A.B. / Horswill, A.R.
History
DepositionJun 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative surface protein MW2416
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,50211
Polymers28,8191
Non-polymers68410
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.600, 70.210, 43.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative surface protein MW2416


Mass: 28818.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus MW2 (bacteria)
Strain: MW2 / Gene: MW2416 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NUV0

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Non-polymers , 5 types, 102 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 100 mM HEPES (pH 7.8), 200 mM Ammonium Sulfate, 25%-33% BCS PEG SMEAR Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793384 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793384 Å / Relative weight: 1
ReflectionResolution: 1.88→52.36 Å / Num. obs: 20226 / % possible obs: 99.79 % / Redundancy: 2 % / Biso Wilson estimate: 20.27 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.06672 / Rrim(I) all: 0.09436 / Net I/σ(I): 5.81
Reflection shellResolution: 1.88→1.947 Å / Rmerge(I) obs: 0.2974 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1980 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→52.36 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 --0.2528
Rwork0.1837 ---
obs-20226 99.79 %-
Refinement stepCycle: LAST / Resolution: 1.88→52.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 26 92 2041

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