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Yorodumi- PDB-6ukd: Co-complex of S. pyogenes 10782 streptopain bound with a nitrile-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ukd | ||||||
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Title | Co-complex of S. pyogenes 10782 streptopain bound with a nitrile-based specific covalent inhibitor | ||||||
Components | Streptopain | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / speb / streptopain / inhibitor / nitrile / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Streptococcus pyogenes ATCC 10782 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.589 Å | ||||||
Authors | Wolan, D.W. / Woehl, J.L. / Kitamura, S. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: An Irreversible Inhibitor to Probe the Role ofStreptococcus pyogenesCysteine Protease SpeB in Evasion of Host Complement Defenses. Authors: Woehl, J.L. / Kitamura, S. / Dillon, N. / Han, Z. / Edgar, L.J. / Nizet, V. / Wolan, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ukd.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ukd.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ukd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ukd_validation.pdf.gz | 756.5 KB | Display | wwPDB validaton report |
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Full document | 6ukd_full_validation.pdf.gz | 756.4 KB | Display | |
Data in XML | 6ukd_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6ukd_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/6ukd ftp://data.pdbj.org/pub/pdb/validation_reports/uk/6ukd | HTTPS FTP |
-Related structure data
Related structure data | 4d8bS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41551.945 Da / Num. of mol.: 1 / Fragment: UNP residues 28-398 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes ATCC 10782 (bacteria) Gene: speB / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0J0, streptopain | ||||
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#2: Chemical | ChemComp-Q9D / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium nitrate, 33% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→46.13 Å / Num. obs: 29409 / % possible obs: 98.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.59→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2644 / CC1/2: 0.826 / Rpim(I) all: 0.222 / Rrim(I) all: 0.477 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4D8B Resolution: 1.589→46.127 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.08 Å2 / Biso mean: 15.5128 Å2 / Biso min: 6.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.589→46.127 Å
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LS refinement shell | Resolution: 1.59→1.65 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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