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Yorodumi- PDB-5l20: Crystal Structure of a Clostripain (BT_0727) from Bacteroides the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l20 | |||||||||
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Title | Crystal Structure of a Clostripain (BT_0727) from Bacteroides thetaiotaomicron ATCC 29148 in Complex with Peptide Inhibitor BTN-VLTK-AOMK | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Clostripain / peptidase / microbiome / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Peptidase C11, clostripain / Clostripain family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Peptide Inhibitor BTN-VLTK-AOMK / Clostripain-related protein Function and homology information | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å | |||||||||
Authors | Wolan, D.W. / Roncase, E.J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal Structure of a Clostripain (BT_0727) from Bacteroides thetaiotaomicron ATCC 29148 in Complex with Peptide Inhibitor BTN-VLTK-AOMK Authors: Wolan, D.W. / Roncase, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l20.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l20.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 5l20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l20_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 5l20_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 5l20_validation.xml.gz | 19 KB | Display | |
Data in CIF | 5l20_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/5l20 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/5l20 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16455.676 Da / Num. of mol.: 1 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_0727 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8A9T8 |
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#2: Protein | Mass: 25966.994 Da / Num. of mol.: 1 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_0727 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8A9T8 |
#3: Protein/peptide | |
#4: Water | ChemComp-HOH / |
Sequence details | the protein is physically cleaved after Arginine 172 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M Na Citrate, 30% PEG 6000, 2M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→43.9 Å / Num. obs: 54597 / % possible obs: 88.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 13.44 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.087 / Rsym value: 0.075 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.774 / % possible all: 44 |
-Processing
Software |
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Refinement | Resolution: 1.45→43.9 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→43.9 Å
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Refine LS restraints |
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LS refinement shell |
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