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Yorodumi- PDB-2uzj: Crystal structure of the mature streptococcal cysteine protease, mSpeB -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uzj | ||||||
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Title | Crystal structure of the mature streptococcal cysteine protease, mSpeB | ||||||
Components | STREPTOPAIN | ||||||
Keywords | HYDROLASE / PROTEINASE / PAPAIN FAMILY / CYSTEINE PROTEASE / DIMER / CLAN CA / EXOTOXIN / FAMILY 10 / PEPTIDASE | ||||||
Function / homology | Function and homology information streptopain / symbiont-mediated suppression of host autophagy / symbiont-induced defense-related programmed cell death / evasion of host immune response / host cell cytosol / : / cysteine-type peptidase activity / toxin activity / host extracellular space / cysteine-type endopeptidase activity ...streptopain / symbiont-mediated suppression of host autophagy / symbiont-induced defense-related programmed cell death / evasion of host immune response / host cell cytosol / : / cysteine-type peptidase activity / toxin activity / host extracellular space / cysteine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PYOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Olsen, J.G. / Dagil, R. / Niclasen, L.M. / Soerensen, O.E. / Kragelund, B.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure of the Mature Streptococcal Cysteine Protease Exotoxin Mspeb in its Active Dimeric Form. Authors: Olsen, J.G. / Dagil, R. / Niclasen, L.M. / Soerensen, O.E. / Kragelund, B.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uzj.cif.gz | 212 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uzj.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 2uzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Data in XML | 2uzj_validation.xml.gz | 11.1 KB | Display | |
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Data in CIF | 2uzj_validation.cif.gz | 933 B | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzj ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzj | HTTPS FTP |
-Related structure data
Related structure data | 1dkiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27611.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PROTEIN WAS PURIFIED FROM NATURAL SOURCE. / Source: (natural) STREPTOCOCCUS PYOGENES (bacteria) / Strain: ALAB49 References: UniProt: Q5X9P3, UniProt: P0C0J0*PLUS, streptopain #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.52 % Description: MOLECULAR REPLACEMENT SEARCH MODEL WAS 1DKI WITHOUT THE PROPEPTIDE |
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Crystal grow | Details: 0.2 M (NH4)2SO4, 0.1 M NA-ACETATE, PH 4.0, 20 % PEG4000. PROTEIN KONCENTRATION WAS 0.07 MM (IN 20 MM NA-ACETATE, PH 5.0). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 15, 2008 / Details: MIRRORS. MSC-CONFOCAL MAXFLUX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→21.48 Å / Num. obs: 63795 / % possible obs: 90.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.32 |
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 0.97 / % possible all: 55.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DKI Resolution: 1.55→21.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.602 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 234A-237A AND 234B-239B ARE ABSENT IN THE MODEL BECAUSE OF INSUFFICIENT ELECTRON DENSITY IN THESE REGIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→21.48 Å
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Refine LS restraints |
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