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- PDB-2au1: Crystal Structure of group A Streptococcus MAC-1 orthorhombic form -

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Basic information

Entry
Database: PDB / ID: 2au1
TitleCrystal Structure of group A Streptococcus MAC-1 orthorhombic form
ComponentsIgG-degrading protease
KeywordsHYDROLASE / MAC-1
Function / homology
Function and homology information


peptidase activity / identical protein binding
Similarity search - Function
Ig protease IdeS / Mac 1 / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / Ig protease IdeS domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAgniswamy, J. / Nagiec, M.J. / Liu, M. / Schuck, P. / Musser, J.M. / Sun, P.D.
CitationJournal: Structure / Year: 2006
Title: Crystal structure of group a streptococcus mac-1: insight into dimer-mediated specificity for recognition of human IgG.
Authors: Agniswamy, J. / Nagiec, M.J. / Liu, M. / Schuck, P. / Musser, J.M. / Sun, P.D.
History
DepositionAug 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgG-degrading protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9372
Polymers32,8591
Non-polymers781
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.865, 87.175, 57.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein IgG-degrading protease / MAC-1


Mass: 32858.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptococcus pyogenes (bacteria) / Strain: MGAS5005 / References: GenBank: 71853263, UniProt: Q7DAM2*PLUS
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: ammonium sulfate, sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 13099 / Num. obs: 11324 / % possible obs: 86.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.4→2.51 Å / % possible all: 5.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 580 Random
Rwork0.216 --
all0.219 13099 -
obs0.217 11324 -
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 4 92 2417

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