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Yorodumi- PDB-5mt8: Structure of E.coli GlpG in complex with peptide derived inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mt8 | ||||||
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Title | Structure of E.coli GlpG in complex with peptide derived inhibitor Ac-RVRHA-cmk | ||||||
Components |
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Keywords | HYDROLASE / Membrane protein / Intramembrane protease | ||||||
Function / homology | Function and homology information rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Providencia stuartii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Vinothkumar, K.R. | ||||||
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 | 5mt8.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mt8.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/5mt8 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/5mt8 | HTTPS FTP |
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-Related structure data
Related structure data | 5mt6C 5mt7C 5mtfC 2xovS 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: 20214.020 Da / Num. of mol.: 1 / Fragment: UNP Residues 92-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glpG, b3424, JW5687 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P09391, rhomboid protease | ||||
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#2: Protein/peptide | Mass: 699.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria) | ||||
#3: Sugar | ChemComp-BNG / #4: Chemical | ChemComp-CL / | #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: 3.5 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M Sodium cholride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→44.9 Å / Num. obs: 21621 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.031 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.593 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XOV Resolution: 1.95→44.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.073 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.27 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→44.9 Å
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Refine LS restraints |
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