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- PDB-7s54: Sortase A from Streptococcus agalactiae with the deltaN188 b7-b8 ... -

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Basic information

Entry
Database: PDB / ID: 7s54
TitleSortase A from Streptococcus agalactiae with the deltaN188 b7-b8 loop sequence from Staphylococcus aureus 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


sortase A / cysteine-type peptidase activity / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Sortase A / Sortase family / Sortase domain superfamily / Sortase domain
Similarity search - Domain/homology
Class A sortase / Sortase A
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 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, sortase A chimera
B: Class A sortase, sortase A chimera


Theoretical massNumber of molelcules
Total (without water)38,0552
Polymers38,0552
Non-polymers00
Water3,837213
1
A: Class A sortase, sortase A chimera


Theoretical massNumber of molelcules
Total (without water)19,0281
Polymers19,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class A sortase, sortase A chimera


Theoretical massNumber of molelcules
Total (without water)19,0281
Polymers19,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.297, 33.520, 115.599
Angle α, β, γ (deg.)90.000, 91.800, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Class A sortase, sortase A chimera / Sortase / Sortase A / LPXTG specific / SrtA / Surface protein sorting A / Sortase / Sortase A / ...Sortase / Sortase A / LPXTG specific / SrtA / Surface protein sorting A / Sortase / Sortase A / LPXTG specific / SrtA


Mass: 19027.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria), (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Gene: srtA, C4618_06055, F5043_06280, GD434_06060, NCTC6175_01342, RDF_0944, srtA, SAOUHSC_02834
Plasmid: pET28a(+) / Strain: NCTC 8325 / PS 47 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H1I052, UniProt: Q2FV99, sortase A
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.81 Å3/Da / Density % sol: 32.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02 MES monohydrate pH 6, 12% (v/v) 2-Propanol, 24% (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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.79→35.631 Å / Num. obs: 25832 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.062 / Rrim(I) all: 0.16 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.835.91.62312920.6650.712183.2
8-106.50.0662370.9980.0270.07199

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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: 3RCC

3rcc


Resolution: 1.794→35.631 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 1254 4.86 %
Rwork0.1845 24534 -
obs0.1877 25788 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.6 Å2 / Biso mean: 25.8436 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.794→35.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 0 213 2753
Biso mean---32.22 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072619
X-RAY DIFFRACTIONf_angle_d0.9433543
X-RAY DIFFRACTIONf_chiral_restr0.054407
X-RAY DIFFRACTIONf_plane_restr0.006449
X-RAY DIFFRACTIONf_dihedral_angle_d15.5911583
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.794-1.86540.3681220.3007250690
1.8654-1.95020.27291410.23242685100
1.9502-2.05310.25451160.19792738100
2.0531-2.18170.24211340.17842751100
2.1817-2.35010.27811570.18582695100
2.3501-2.58650.27021440.19072760100
2.5865-2.96060.2811440.19022761100
2.9606-3.72950.22391600.16882773100
3.7295-100.21451360.16362865100

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