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Yorodumi- PDB-4yec: Crystal structure of a clostripain (PARMER_00083) from Parabacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yec | |||||||||
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Title | Crystal structure of a clostripain (PARMER_00083) from Parabacteroides merdae ATCC 43184 in complex with peptide inhibitor Ac-VLTK-AOMK | |||||||||
Components |
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Keywords | Unknown Function/Inhibitor / clostripain / microbiome / secreted protease / inhibitor / Unknown Function-Inhibitor complex | |||||||||
Function / homology | Rossmann fold - #11970 / Peptidase C11, clostripain / Clostripain family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Peptide inhibitor Ac-VLTK-AOMK / Clostripain family Function and homology information | |||||||||
Biological species | Parabacteroides merdae ATCC 43184 (bacteria) unidentified (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | |||||||||
Authors | Wolan, D.W. / Gonzalez-Paez, G.E. / Chatterjee, S. | |||||||||
Funding support | United States, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Substrate Profiling and High Resolution Co-complex Crystal Structure of a Secreted C11 Protease Conserved across Commensal Bacteria. Authors: Roncase, E.J. / Moon, C. / Chatterjee, S. / Gonzalez-Paez, G.E. / Craik, C.S. / O'Donoghue, A.J. / 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 | 4yec.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yec.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4yec ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yec | HTTPS FTP |
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-Related structure data
Related structure data | 3uwsS 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
#1: Protein | Mass: 14048.896 Da / Num. of mol.: 1 / Fragment: UNP residues 23-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parabacteroides merdae ATCC 43184 (bacteria) Gene: PARMER_00083 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A7A9N3 |
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#2: Protein | Mass: 27534.025 Da / Num. of mol.: 1 / Fragment: UNP residues 148-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parabacteroides merdae ATCC 43184 (bacteria) Gene: PARMER_00083 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A7A9N3 |
#3: Protein/peptide | |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.05M NH4CL, 20.0% PEG-3350, NO BUFFER |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→36.61 Å / Num. obs: 90762 / % possible obs: 78.9 % / Redundancy: 3 % / Biso Wilson estimate: 14.66 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9.32 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.1 / % possible all: 14.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UWS Resolution: 1.12→36.61 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.62 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→36.61 Å
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Refine LS restraints |
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LS refinement shell |
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