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- PDB-4yec: Crystal structure of a clostripain (PARMER_00083) from Parabacter... -
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Open data
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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 | |||||||||
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![]() | 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![]() | |||||||||
Biological species | ![]() unidentified (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wolan, D.W. / Gonzalez-Paez, G.E. / Chatterjee, S. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.9 KB | Display | ![]() |
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PDB format | ![]() | 128.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Gene: PARMER_00083 Production host: ![]() ![]() 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.) ![]() Gene: PARMER_00083 Production host: ![]() ![]() References: UniProt: A7A9N3 |
#3: Protein/peptide | |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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