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Yorodumi- PDB-5mt7: Structure of E.coli GlpG in complex with peptide derived inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mt7 | ||||||
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Title | Structure of E.coli GlpG in complex with peptide derived inhibitor Ac-VRHA-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: 2.05 Å | ||||||
Authors | Vinothkumar, K.R. | ||||||
Funding support | United Kingdom, 1items
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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 | 5mt7.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mt7.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/5mt7 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/5mt7 | HTTPS FTP |
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-Related structure data
Related structure data | 5mt6C 5mt8C 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: 20457.234 Da / Num. of mol.: 1 / Fragment: UNP Residues 91-271 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: 542.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Providencia stuartii (bacteria) |
#3: 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: 63.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M sodium chloride |
-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: 2.05→44.9 Å / Num. obs: 18936 / % possible obs: 99.7 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.795 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XOV Resolution: 2.05→44.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.695 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.135 / 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: 59.712 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→44.9 Å
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Refine LS restraints |
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