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- PDB-2avw: Crystal structure of monoclinic form of streptococcus Mac-1 -

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Basic information

Entry
Database: PDB / ID: 2avw
TitleCrystal structure of monoclinic form of streptococcus Mac-1
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
: / Ig protease IdeS domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 30, 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 1.3Oct 20, 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 1.4Feb 14, 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: IgG-degrading protease
B: IgG-degrading protease
C: IgG-degrading protease
D: IgG-degrading protease
E: IgG-degrading protease
F: IgG-degrading protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,17913
Polymers210,5116
Non-polymers6687
Water17,276959
1
A: IgG-degrading protease
B: IgG-degrading protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3624
Polymers70,1702
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: IgG-degrading protease
D: IgG-degrading protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3624
Polymers70,1702
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: IgG-degrading protease
F: IgG-degrading protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4555
Polymers70,1702
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.986, 65.464, 137.244
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
IgG-degrading protease


Mass: 35085.152 Da / Num. of mol.: 6 / Mutation: C94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: MGAS5005 / Gene: mac / Production host: Escherichia coli (E. coli) / References: GenBank: 71910481, UniProt: Q7DAM2*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / 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: 2.2 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 1.5M ammonium sulfate and 0.1M Ssodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 123851 / Num. obs: 104599 / % possible obs: 84.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.09 Å / % possible all: 7.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 5283 Random
Rwork0.218 --
all0.224 123851 -
obs0.22 104599 -
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13895 0 36 959 14890

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