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Yorodumi- PDB-6n9j: X-ray structure of a secreted C11 cysteine protease from Bacteroi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n9j | |||||||||
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Title | X-ray structure of a secreted C11 cysteine protease from Bacteroides thetaiotaomicron in complex with an irreversible peptide inhibitor | |||||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / C11 protease / secreted / covalent peptide inhibitor / microbiome / commensal / HYDROLASE / hydrolase-hydrolase inhibitor complex | |||||||||
Function / homology | Peptidase C11, clostripain / Clostripain family / Clostripain-related protein Function and homology information | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | |||||||||
Authors | Wolan, D.W. / Gonzalez-Paez, G.E. / Roncase, E.J. | |||||||||
Citation | Journal: Biochemistry / Year: 2019 Title: X-ray Structures of Two Bacteroides thetaiotaomicron C11 Proteases in Complex with Peptide-Based Inhibitors. Authors: Roncase, E.J. / Gonzalez-Paez, G.E. / 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 | 6n9j.cif.gz | 292.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n9j.ent.gz | 234.9 KB | Display | PDB format |
PDBx/mmJSON format | 6n9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/6n9j ftp://data.pdbj.org/pub/pdb/validation_reports/n9/6n9j | HTTPS FTP |
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-Related structure data
Related structure data | 6nagC 4yecS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42445.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_1308 / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q8A866 #2: Protein/peptide | Mass: 483.645 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.3 Å3/Da / Density % sol: 46.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES, pH 7.0, 1M LiCl, 26% PEG 6000 |
-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: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014 / Details: Rh coated flat |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→49.482 Å / Num. obs: 40736 / % possible obs: 93.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.073 / Rrim(I) all: 0.094 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.17→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.238 / Num. unique obs: 3313 / Rpim(I) all: 0.179 / Rrim(I) all: 0.3 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YEC Resolution: 2.17→49.482 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→49.482 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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