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- PDB-1y08: Structure of the Streptococcal Endopeptidase IdeS, a Novel Cystei... -

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Basic information

Entry
Database: PDB / ID: 1y08
TitleStructure of the Streptococcal Endopeptidase IdeS, a Novel Cysteine Proteinase with Strict Specificity for IgG
Componentshypothetical protein SPy0861
KeywordsHYDROLASE / cysteine proteinase / papain-like fold with major insertions
Function / homologyIg protease IdeS / Mac 1 / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / peptidase activity / Alpha-Beta Complex / Alpha Beta / Sib38
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å
AuthorsWenig, K. / Chatwell, L. / von Pawel-Rammingen, U. / Bjoerck, L. / Huber, R. / Sondermann, P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Structure of the streptococcal endopeptidase IdeS, a cysteine proteinase with strict specificity for IgG
Authors: Wenig, K. / Chatwell, L. / von Pawel-Rammingen, U. / Bjoerck, L. / Huber, R. / Sondermann, P.
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein SPy0861
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4902
Polymers36,3941
Non-polymers961
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.371, 86.829, 57.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer

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Components

#1: Protein hypothetical protein SPy0861 / IdeS / IgG-degrading enzyme


Mass: 36393.676 Da / Num. of mol.: 1 / Fragment: residues 49-339 / Mutation: C94S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q9F1R7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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: 2

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: PEG 2000 MME, ammonium sulfate, sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.97910, 0.95, 0.97935, 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: May 9, 2004
RadiationMonochromator: ROEMO type double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.951
30.979351
41.051
ReflectionResolution: 1.93→20 Å / Num. all: 186153 / Num. obs: 24440 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.58 Å2 / Rmerge(I) obs: 0.063
Reflection shellResolution: 1.93→2 Å / Rmerge(I) obs: 0.266 / % possible all: 99.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.93→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 1911 RANDOM
Rwork0.196 --
all-24440 -
obs-24385 -
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 5 206 2491
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0086
X-RAY DIFFRACTIONc_angle_deg1.37

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