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Yorodumi- PDB-5mtf: A modular route to novel potent and selective inhibitors of rhomb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mtf | ||||||
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Title | A modular route to novel potent and selective inhibitors of rhomboid intramembrane proteases | ||||||
Components |
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Keywords | HYDROLASE / Rhomboid protease / specificity / inhibition / ketoamide | ||||||
Function / homology | Function and homology information rhomboid protease / membrane => GO:0016020 / serine-type endopeptidase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli O45:K1 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å | ||||||
Authors | Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D. / Bachovchin, D. ...Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D. / Bachovchin, D. / Lepsik, M. / Majer, P. / Strisovsky, K. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2017 Title: General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases. Authors: Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Began, J. / Skerle, J. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D.C. / Bachovchin, D.A. / ...Authors: Ticha, A. / Stanchev, S. / Vinothkumar, K.R. / Mikles, D.C. / Pachl, P. / Began, J. / Skerle, J. / Svehlova, K. / Nguyen, M.T.N. / Verhelst, S.H.L. / Johnson, D.C. / Bachovchin, D.A. / Lepsik, M. / Majer, P. / Strisovsky, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mtf.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mtf.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mtf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/5mtf ftp://data.pdbj.org/pub/pdb/validation_reports/mt/5mtf | HTTPS FTP |
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-Related structure data
Related structure data | 5mt6C 5mt7C 5mt8C 4qnzS 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: 21513.568 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria) Strain: S88 / ExPEC / Gene: glpG, ECS88_3813 / Plasmid: pET25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: B7MDQ0, rhomboid protease | ||||
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#2: Protein/peptide | Mass: 814.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | #4: Sugar | ChemComp-BNG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3M NH4Cl, 25mM Bis Tris pH7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918408 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918408 Å / Relative weight: 1 |
Reflection | Resolution: 1.787→44.97 Å / Num. obs: 28202 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 37.88 Å2 / Net I/σ(I): 18.64 |
Reflection shell | Resolution: 1.79→1.9 Å / Redundancy: 4.95 % / Mean I/σ(I) obs: 1.86 / % possible all: 99.6 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.505
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QNZ Resolution: 1.79→44.97 Å / SU B: 4.53 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Displacement parameters | Biso mean: 35.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→44.97 Å
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