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- PDB-7t8y: Structure of Class A sortase from Streptococcus pyogenes bound to... -

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Basic information

Entry
Database: PDB / ID: 7t8y
TitleStructure of Class A sortase from Streptococcus pyogenes bound to lipid II mimetic, LPATA: Thr-in conformation
Components
  • ACE-ALA-ZGL-LYS-DAL-DAL
  • BE2-LEU-PRO-ALA-THR-ALA-ALA
  • Sortase
KeywordsHYDROLASE / sortase-fold / sortase / eight-stranded beta barrel / transpeptidase / housekeeping sortase / surface protein
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis
Similarity search - Function
Sortase A / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus pyogenes (bacteria)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPiper, I.M. / Antos, J.M. / Amacher, J.F.
Funding support1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2044958
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structures of Streptococcus pyogenes class A sortase in complex with substrate and product mimics provide key details of target recognition.
Authors: Johnson, D.A. / Piper, I.M. / Vogel, B.A. / Jackson, S.N. / Svendsen, J.E. / Kodama, H.M. / Lee, D.E. / Lindblom, K.M. / McCarty, J. / Antos, J.M. / Amacher, J.F.
History
DepositionDec 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 12, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase
B: BE2-LEU-PRO-ALA-THR-ALA-ALA
D: ACE-ALA-ZGL-LYS-DAL-DAL


Theoretical massNumber of molelcules
Total (without water)19,7973
Polymers19,7973
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography confirmed monomeric protein.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.302, 57.733, 72.251
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 Sortase / Sortase A


Mass: 18621.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: srtA_1, srtA, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY92_04850, GTK43_04765, GTK52_04270, GTK54_03910, GUA39_04435, IB935_04675, ...Gene: srtA_1, srtA, srtA_2, E0F66_05345, E0F67_00760, FGO82_09960, FNL90_04725, FNL91_04720, GQ677_05600, GQR49_04420, GQY92_04850, GTK43_04765, GTK52_04270, GTK54_03910, GUA39_04435, IB935_04675, IB936_04605, IB937_04535, IB938_05195, KUN2590_09100, KUN4944_08330, SAMEA1407055_00305, SAMEA1711581_00311, SAMEA1711644_00960, SPNIH34_10200, SPNIH35_09070
Plasmid: pET18a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4U7I1I9
#2: Protein/peptide BE2-LEU-PRO-ALA-THR-ALA-ALA


Type: Peptide-like / Class: Inhibitor / Mass: 661.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) / References: BIRD: PRD_002489
#3: Protein/peptide ACE-ALA-ZGL-LYS-DAL-DAL


Type: Peptide-like / Class: Inhibitor / Mass: 514.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) / References: BIRD: PRD_002489
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 31.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.15 M Na acetate, 26% PEG 8000, 0.1 M Tris pH 6

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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: Oct 14, 2021
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.8→45.103 Å / Num. obs: 25396 / % possible obs: 98.9 % / Redundancy: 5.87 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 0.999 / Rsym value: 0.074 / Net I/σ(I): 15.55
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 2.47 / Num. unique obs: 4137 / CC1/2: 0.84 / Rsym value: 0.53 / % possible all: 94

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 1.8→45.103 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 684 4.98 %
Rwork0.1745 13055 -
obs0.176 13739 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.64 Å2 / Biso mean: 24.0546 Å2 / Biso min: 6.98 Å2
Refinement stepCycle: final / Resolution: 1.8→45.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 83 129 1432
Biso mean--39.17 33.72 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061325
X-RAY DIFFRACTIONf_angle_d1.1351797
X-RAY DIFFRACTIONf_chiral_restr0.08208
X-RAY DIFFRACTIONf_plane_restr0.006232
X-RAY DIFFRACTIONf_dihedral_angle_d19.18756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8002-1.93920.26231330.2054244596
1.9392-2.13430.21211340.1732604100
2.1343-2.44310.21581420.17232595100
2.4431-3.0780.22111390.18652638100
3.078-45.1030.18211360.16452773100

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