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- PDB-7s56: Sortase A from Streptococcus agalactiae, residues 79-247 -

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Basic information

Entry
Database: PDB / ID: 7s56
TitleSortase A from Streptococcus agalactiae, residues 79-247
ComponentsClass A sortase
KeywordsHYDROLASE / sortase-fold / sortase / eight-standed 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 agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGao, M. / Kodama, H.M. / 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


Theoretical massNumber of molelcules
Total (without water)18,4181
Polymers18,4181
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size exclusion chromatography to isolate monomeric species.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.134, 54.635, 60.246
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 / Sortase A / LPXTG specific / SrtA


Mass: 18417.990 Da / Num. of mol.: 1 / Fragment: UNP residues 79-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria)
Gene: srtA, C4618_06055, F5043_06280, GD434_06060, NCTC6175_01342, RDF_0944
Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H1I052
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 20% (v/v) 2-Propanol, 0.1 M MES monohydrate pH 6.1, 20% (w/v) PEG monomethyl ether 2000

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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: Apr 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: 1.4→40.47 Å / Num. obs: 29340 / % possible obs: 99.58 % / Redundancy: 12 % / Biso Wilson estimate: 14.58 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.06 / Rsym value: 0.05 / Net I/σ(I): 29.08
Reflection shellResolution: 1.42→1.5 Å / Mean I/σ(I) obs: 3.78 / Num. unique obs: 4598 / CC1/2: 0.953 / Rrim(I) all: 0.727 / Rsym value: 0.694

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RCC

3rcc


Resolution: 1.4→40.47 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2066 1463 4.99 %
Rwork0.1854 27877 -
obs0.1864 29340 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.62 Å2 / Biso mean: 17.5254 Å2 / Biso min: 8.11 Å2
Refinement stepCycle: final / Resolution: 1.4→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 206 1465
Biso mean---28.85 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011303
X-RAY DIFFRACTIONf_angle_d1.1021765
X-RAY DIFFRACTIONf_dihedral_angle_d6.244174
X-RAY DIFFRACTIONf_chiral_restr0.089206
X-RAY DIFFRACTIONf_plane_restr0.007224
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.450.34171330.3206267897
1.45-1.510.36681260.33892770100
1.51-1.570.3661480.29792767100
1.57-1.660.21351420.20032754100
1.66-1.760.21161530.18332770100
1.76-1.90.22891340.20572776100
1.9-2.090.18591460.1622775100
2.09-2.390.20671780.1673277899
2.39-3.010.20781510.17142839100
3.01-100.15751520.15752970100

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