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- PDB-7s53: Structure of Sortase A from Streptococcus pyogenes with the b7-b8... -

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Basic information

Entry
Database: PDB / ID: 7s53
TitleStructure of Sortase A from Streptococcus pyogenes with the b7-b8 loop sequence from Listeria monocytogenes Sortase A
ComponentsClass A sortase, sortase A chimera
KeywordsHYDROLASE / sortase-fold / sortase / eight-stranded beta barrel / transpeptidase / housekeeping sortase / surface protein
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / plasma membrane
Similarity search - Function
Sortase A / Sortase family / Sortase domain superfamily / Sortase domain
Similarity search - Domain/homology
Biological speciesStreptococcus pyogenes (bacteria)
Listeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJohnson, D.A. / Svendsen, J.E. / Antos, J.M. / Amacher, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2044958 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes.
Authors: Gao, M. / Johnson, D.A. / Piper, I.M. / Kodama, H.M. / Svendsen, J.E. / Tahti, E. / Longshore-Neate, F. / Vogel, B. / Antos, J.M. / Amacher, J.F.
History
DepositionSep 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class A sortase, sortase A chimera


Theoretical massNumber of molelcules
Total (without water)18,7641
Polymers18,7641
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography confirmed monomeric species.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.294, 58.137, 73.269
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 Class A sortase, sortase A chimera / Sortase A / Sortase protein SrtA


Mass: 18764.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria), (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (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, srtA, lmo0929
Plasmid: pET28a(+) / Strain: ATCC BAA-679 / EGD-e / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A4U7I1I9, UniProt: Q8Y8H5, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% (w/v) PEG 8000, 0.2 M sodium acetate, 0.1 M Tris pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2020
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.6→45.542 Å / Num. obs: 20018 / % possible obs: 99.8 % / Redundancy: 12.3 % / Biso Wilson estimate: 15.24 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.033 / Rrim(I) all: 0.111 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.63100.5089740.9190.1680.53699.4
8-1010.60.0431600.9990.0130.04599.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 1.6→45.542 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3006 960 4.89 %
Rwork0.263 18675 -
obs0.2648 19635 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.24 Å2 / Biso mean: 18.3345 Å2 / Biso min: 3.09 Å2
Refinement stepCycle: final / Resolution: 1.6→45.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 0 228 1442
Biso mean---25.72 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061235
X-RAY DIFFRACTIONf_angle_d0.9251670
X-RAY DIFFRACTIONf_chiral_restr0.058194
X-RAY DIFFRACTIONf_plane_restr0.007213
X-RAY DIFFRACTIONf_dihedral_angle_d15.488744
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6001-1.68440.25471260.19472673100
1.6844-1.790.27961330.2796265899
1.79-1.92820.37781360.3575252294
1.9282-2.12220.42961290.3491255795
2.1222-2.42930.32691460.3066267199
2.4293-3.06050.30541430.25762722100
3.0605-45.5420.23351470.19782872100

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