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- PDB-8g1l: Lectin domain of Aap (Staphylococcus epidermidis Accumulation Ass... -

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Basic information

Entry
Database: PDB / ID: 8g1l
TitleLectin domain of Aap (Staphylococcus epidermidis Accumulation Associated Protein)
ComponentsAccumulation associated protein
KeywordsCELL ADHESION / bacterial lectin / cell wall-attached protein / glycan binding
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
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 ...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
Accumulation associated protein
Similarity search - Component
Biological speciesStaphylococcus epidermidis RP62A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.06 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: To Be Published
Title: Mechanistic basis of staphylococcal interspecies competition for skin colonization
Authors: Maciag, J.J. / Herr, A.B.
History
DepositionFeb 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Accumulation associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7178
Polymers27,4381
Non-polymers2797
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, assay for oligomerization, sedimentation velocity analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.664, 68.573, 109.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Accumulation associated protein


Mass: 27437.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis RP62A (bacteria)
Gene: aap, SERP2398 / Plasmid: pDest-HisMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BLR / References: UniProt: Q5HKE8

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Non-polymers , 5 types, 352 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na Acetate (pH 4.5), 22.5% BCS PEG SMEAR High (Molecular Dimensions, CalibreScientific), pentanediol and 100 mM BisTris (pH 6.5)

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Data collection

DiffractionMean temperature: 183 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9778 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.06→42.7658 Å / Num. obs: 121879 / % possible obs: 99.65 % / Redundancy: 8.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09085 / Rpim(I) all: 0.03388 / Rrim(I) all: 0.09719 / Net I/σ(I): 14.88
Reflection shellResolution: 1.06→1.098 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.5542 / Mean I/σ(I) obs: 4.39 / Num. unique obs: 11899 / CC1/2: 0.911 / Rpim(I) all: 0.2158 / Rrim(I) all: 0.596 / % possible all: 98.48

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
HKL-3000data reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.06→42.7658 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 9.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1263 2000 1.64 %
Rwork0.1165 --
obs0.1167 121846 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.06→42.7658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 14 345 2277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062076
X-RAY DIFFRACTIONf_angle_d1.0232844
X-RAY DIFFRACTIONf_dihedral_angle_d8.6811135
X-RAY DIFFRACTIONf_chiral_restr0.09302
X-RAY DIFFRACTIONf_plane_restr0.008389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.08640.14171380.13288292X-RAY DIFFRACTION97
1.0864-1.11570.12931430.11738516X-RAY DIFFRACTION100
1.1157-1.14860.12891400.11058445X-RAY DIFFRACTION100
1.1486-1.18570.1291420.10318493X-RAY DIFFRACTION100
1.1857-1.2280.12551420.1018530X-RAY DIFFRACTION100
1.228-1.27720.13711420.10078504X-RAY DIFFRACTION100
1.2772-1.33530.10971430.10068513X-RAY DIFFRACTION100
1.3353-1.40570.10731420.09898552X-RAY DIFFRACTION100
1.4057-1.49380.12371430.10148560X-RAY DIFFRACTION100
1.4938-1.60920.1161430.10248569X-RAY DIFFRACTION100
1.6092-1.77110.12431430.10658590X-RAY DIFFRACTION100
1.7711-2.02740.12671440.11448605X-RAY DIFFRACTION100
2.0274-2.55420.1241460.12178692X-RAY DIFFRACTION99
2.5542-42.76580.13371490.13548985X-RAY DIFFRACTION99

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