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- PDB-8snq: Streptococcus pyogenes Sortase A (SrtA) with the F145E mutation -

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Basic information

Entry
Database: PDB / ID: 8snq
TitleStreptococcus pyogenes Sortase A (SrtA) with the F145E mutation
ComponentsSortase
KeywordsHYDROLASE / SORTASE A / SORTASE PROTEIN SRTA / ENZYME / TRANSPEPTIDASE
Function / homologySortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / Sortase
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKodama, H.M. / Amacher, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2044958 United States
CitationJournal: To Be Published
Title: Streptococcus pyogenes Sortase A (SrtA) with the F145E mutation
Authors: Kodama, H.M. / Amacher, J.F.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase


Theoretical massNumber of molelcules
Total (without water)18,6031
Polymers18,6031
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomeric peak isolated following gel filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.222, 34.299, 71.229
Angle α, β, γ (deg.)90.000, 97.410, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Sortase /


Mass: 18603.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Class A sortase / Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: srtA_1 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4U7I1I9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.87 Å3/Da / Density % sol: 34.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 24% (w/v) PEG 8000, 0.15 M sodium acetate, 0.1 M Tris pH 6.0

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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: Mar 25, 2023
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.5→35.32 Å / Num. obs: 21772 / % possible obs: 97.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.56 Å2 / CC1/2: 0.999 / Rsym value: 0.06 / Net I/σ(I): 18.08
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 3148 / CC1/2: 0.804 / Rsym value: 0.632 / % possible all: 87.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1_4487refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.32 Å / SU ML: 0.1584 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2072 2138 9.82 %
Rwork0.181 19634 -
obs0.1835 21772 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.57 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1305 0 0 169 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681325
X-RAY DIFFRACTIONf_angle_d0.93551795
X-RAY DIFFRACTIONf_chiral_restr0.0621210
X-RAY DIFFRACTIONf_plane_restr0.0069233
X-RAY DIFFRACTIONf_dihedral_angle_d5.8322180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.30781280.27951030X-RAY DIFFRACTION78.94
1.53-1.570.26991140.24431215X-RAY DIFFRACTION90.65
1.57-1.620.21781600.22731305X-RAY DIFFRACTION99.46
1.62-1.660.25321660.2141307X-RAY DIFFRACTION99.8
1.66-1.720.25871380.20091330X-RAY DIFFRACTION100
1.72-1.780.25381330.20721334X-RAY DIFFRACTION99.93
1.78-1.850.23281490.2041326X-RAY DIFFRACTION100
1.85-1.930.20791480.17741320X-RAY DIFFRACTION100
1.93-2.040.22051470.16491338X-RAY DIFFRACTION100
2.04-2.160.21061300.17261332X-RAY DIFFRACTION100
2.16-2.330.22141400.16471336X-RAY DIFFRACTION100
2.33-2.560.22541560.17821359X-RAY DIFFRACTION100
2.56-2.940.23261630.18681309X-RAY DIFFRACTION100
2.94-3.70.16821600.16921349X-RAY DIFFRACTION100
3.7-100.15161060.16631444X-RAY DIFFRACTION100

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