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Yorodumi- PDB-6nag: X-ray structure of a secreted C11 cysteine protease from Bacteroi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nag | ||||||
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Title | X-ray structure of a secreted C11 cysteine protease from Bacteroides thetaiotaomicron "iotapain | ||||||
Components | Clostripain-related protein | ||||||
Keywords | HYDROLASE / C11 protease / secreted / microbiome / commensal | ||||||
Function / homology | Peptidase C11, clostripain / Clostripain family / Prokaryotic membrane lipoprotein lipid attachment site profile. / PROLINE / Clostripain-related protein Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.683 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 | 6nag.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nag.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 6nag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/6nag ftp://data.pdbj.org/pub/pdb/validation_reports/na/6nag | HTTPS FTP |
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-Related structure data
Related structure data | 6n9jC 5l20S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41304.375 Da / Num. of mol.: 2 / Mutation: R154A 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 / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: Q8A9T8 #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: 4.8 Å3/Da / Density % sol: 74.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Na Citrate, pH 5.0, 50% MPD, 10 mM L-Proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2017 / Details: Rh coated |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→45.52 Å / Num. obs: 47832 / % possible obs: 98.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.8 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.081 / Rrim(I) all: 0.178 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.68→2.73 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2368 / CC1/2: 0.719 / Rpim(I) all: 0.339 / Rrim(I) all: 0.735 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L20 Resolution: 2.683→45.517 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.93 / 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: 2.683→45.517 Å
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Refine LS restraints |
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LS refinement shell |
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