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- PDB-8t8g: C208A Streptococcus pyogenes Sortase A (spySrtA) bound to LPALA p... -

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Basic information

Entry
Database: PDB / ID: 8t8g
TitleC208A Streptococcus pyogenes Sortase A (spySrtA) bound to LPALA peptide
Components
  • LEU-PRO-ALA-LEU-ALA-GLY
  • Sortase
KeywordsHYDROLASE / SORTASE-FOLD / SORTASE / EIGHT-STRANDED BETA BARREL / TRANSPEPTIDASE / HOUSEKEEPING SORTASE / SURFACE PROTEIN
Function / homologySortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / Sortase
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKodama, H.M. / Amacher, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2044958 United States
CitationJournal: Rsc Chem Biol / Year: 2024
Title: A unique binding mode of P1' Leu-containing target sequences for Streptococcus pyogenes sortase A results in alternative cleavage.
Authors: Vogel, B.A. / Blount, J.M. / Kodama, H.M. / Goodwin-Rice, N.J. / Andaluz, D.J. / Jackson, S.N. / Antos, J.M. / Amacher, J.F.
History
DepositionJun 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 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: Sortase
B: LEU-PRO-ALA-LEU-ALA-GLY


Theoretical massNumber of molelcules
Total (without water)19,1302
Polymers19,1302
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-6 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.114, 57.477, 71.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Sortase / / Sortase A / Sortase protein SrtA


Mass: 18589.051 Da / Num. of mol.: 1 / Mutation: C208A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: srtA, srtA_1, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY31_04460, GQY92_04850, GTK43_04765, GTK52_04270, GTK53_04530, GTK54_03910, ...Gene: srtA, srtA_1, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY31_04460, GQY92_04850, GTK43_04765, GTK52_04270, GTK53_04530, GTK54_03910, GUA39_04435, IB935_04675, IB936_04605, IB937_04535, IB938_05195, KUN2590_09100, KUN4944_08330, MGAS2221_0893, SAMEA1407055_00305, SAMEA1711644_00960, SAMEA3918953_00457, SPNIH34_10200, SPNIH35_09070
Plasmid: pET28a(+) / Cell (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4U7I1I9
#2: Protein/peptide LEU-PRO-ALA-LEU-ALA-GLY


Mass: 540.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Tris, 30% PEG 8000, 0.25 M sodium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2023
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.5→35.66 Å / Num. obs: 43124 / % possible obs: 99.3 % / Redundancy: 6.28 % / Biso Wilson estimate: 17.1 Å2 / CC1/2: 1 / Rsym value: 0.034 / Net I/σ(I): 27.2
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.27 / Num. unique obs: 6735 / CC1/2: 0.928 / Rsym value: 0.355 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHENIXphasing
XDSdata reduction
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.66 Å / SU ML: 0.1543 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 2299 9.98 %
Rwork0.19 20735 -
obs0.1926 23034 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 0 126 1375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611277
X-RAY DIFFRACTIONf_angle_d0.91641730
X-RAY DIFFRACTIONf_chiral_restr0.0641203
X-RAY DIFFRACTIONf_plane_restr0.0084222
X-RAY DIFFRACTIONf_dihedral_angle_d6.165172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.31411270.27251194X-RAY DIFFRACTION94.83
1.53-1.570.26661400.22741267X-RAY DIFFRACTION97.84
1.57-1.610.26431230.21303X-RAY DIFFRACTION100
1.61-1.650.24711370.19221282X-RAY DIFFRACTION100
1.65-1.70.24141450.19921287X-RAY DIFFRACTION100
1.7-1.750.25571320.21031287X-RAY DIFFRACTION99.93
1.75-1.820.23271400.20671276X-RAY DIFFRACTION99.93
1.82-1.890.23681470.19971294X-RAY DIFFRACTION100
1.89-1.980.24961410.19911294X-RAY DIFFRACTION99.86
1.98-2.080.2071390.19081310X-RAY DIFFRACTION99.86
2.08-2.210.22391680.19811256X-RAY DIFFRACTION100
2.21-2.380.2161300.1951314X-RAY DIFFRACTION99.65
2.38-2.620.24451590.19871306X-RAY DIFFRACTION100
2.62-30.21371540.19371306X-RAY DIFFRACTION100
3-3.780.18921440.17111355X-RAY DIFFRACTION100
3.78-35.660.18491730.17351404X-RAY DIFFRACTION100

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