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Yorodumi- PDB-4qo0: Crystal structure of rhomboid intramembrane protease GlpG in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qo0 | ||||||
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Title | Crystal structure of rhomboid intramembrane protease GlpG in complex with peptide derived inhibitor Ac-FATA-cmk | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / alpha-helical / Rhomboid intramembrane protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Rhomboid-like fold / Rhomboid-like / Up-down Bundle / Mainly Alpha / ACE-PHE-ALA-THR-ALA-0QE / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Zoll, S. / Strisovsky, K. | ||||||
Citation | Journal: Embo J. / Year: 2014 Title: Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate-peptide complex structures. Authors: Zoll, S. / Stanchev, S. / Began, J. / Skerle, J. / Lepsik, M. / Peclinovska, L. / 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 | 4qo0.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qo0.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/4qo0 ftp://data.pdbj.org/pub/pdb/validation_reports/qo/4qo0 | HTTPS FTP |
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-Related structure data
Related structure data | 4qnzC 4qo2C 2ic8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22737.914 Da / Num. of mol.: 1 / Fragment: Rhomboid protease GlpG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: C41 / Gene: glpG, BN896_3117 / Production host: Escherichia coli (E. coli) / References: UniProt: U6NA71, rhomboid protease | ||
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#2: Protein/peptide | | ||
#3: Chemical | ChemComp-CL / | ||
#4: Sugar | #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: 3.93 Å3/Da / Density % sol: 68.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 10% PEG 8000, 0.1 M CHES pH 9.5, 0.2 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→51.79 Å / Num. all: 8094 / Num. obs: 8086 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.9→3.003 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IC8 Resolution: 2.9→51.79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.636 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.534 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.105 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→51.79 Å
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Refine LS restraints |
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