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- PDB-7s51: Structure of C208A Sortase A from Streptococcus pyogenes bound to... -

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Basic information

Entry
Database: PDB / ID: 7s51
TitleStructure of C208A Sortase A from Streptococcus pyogenes bound to LPATA peptide
Components
  • LEU-PRO-ALA-THR-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: 1.4 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: 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
DepositionSep 9, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase
B: Sortase
C: LEU-PRO-ALA-THR-ALA
D: LEU-PRO-ALA-THR-ALA


Theoretical massNumber of molelcules
Total (without water)38,9064
Polymers38,9064
Non-polymers00
Water4,630257
1
A: Sortase
C: LEU-PRO-ALA-THR-ALA


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-3 kcal/mol
Surface area7820 Å2
MethodPISA
2
B: Sortase
D: LEU-PRO-ALA-THR-ALA


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-4 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.979, 64.566, 75.019
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 / Sortase protein SrtA


Mass: 18589.051 Da / Num. of mol.: 2 / 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(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4U7I1I9
#2: Protein/peptide LEU-PRO-ALA-THR-ALA


Mass: 864.000 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Tris pH 6, 34% (w/v) PEG 8000, 0.1 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 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: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.4→48.94 Å / Num. obs: 57131 / % possible obs: 99.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 10.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.028 / Rrim(I) all: 0.101 / Net I/σ(I): 13.6 / Num. measured all: 719759 / Scaling rejects: 4283
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.4-1.429.80.47928550.9530.160.50699.1
7.54-1011.90.0924390.9970.0270.09699.9

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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: 1.4→48.937 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 2838 4.98 %
Rwork0.2134 54151 -
obs0.2146 56989 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.65 Å2 / Biso mean: 14.4023 Å2 / Biso min: 3.41 Å2
Refinement stepCycle: final / Resolution: 1.4→48.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 0 257 2894
Biso mean---24.22 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072732
X-RAY DIFFRACTIONf_angle_d0.9883708
X-RAY DIFFRACTIONf_chiral_restr0.082429
X-RAY DIFFRACTIONf_plane_restr0.005483
X-RAY DIFFRACTIONf_dihedral_angle_d18.741004
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.42380.30691420.2835263299
1.4238-1.44970.25461420.23992666100
1.4497-1.47760.27161400.21792708100
1.4776-1.50770.24271680.20542624100
1.5077-1.54050.24021510.19992678100
1.5405-1.57630.20011200.18912688100
1.5763-1.61580.25171380.19322676100
1.6158-1.65950.23091240.20142707100
1.6595-1.70830.231400.20472700100
1.7083-1.76340.26121060.20162705100
1.7634-1.82650.21891610.2082696100
1.8265-1.89960.1921170.192271999
1.8996-1.98610.24721320.19492692100
1.9861-2.09080.21941620.2021268499
2.0908-2.22180.22431610.2072678100
2.2218-2.39330.21251270.20962727100
2.3933-2.63410.25461680.22242721100
2.6341-3.01520.24591610.2292743100
3.0152-3.79870.22871280.21292799100
3.7987-48.9370.25671500.23432908100

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