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Yorodumi- PDB-2irv: Crystal structure of GlpG, a rhomboid intramembrane serine protease -
+Open data
-Basic information
Entry | Database: PDB / ID: 2irv | ||||||
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Title | Crystal structure of GlpG, a rhomboid intramembrane serine protease | ||||||
Components | Protein glpG | ||||||
Keywords | MEMBRANE PROTEIN / cavity / ser-his dyad | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.3 Å | ||||||
Authors | Bibi, E. / Fass, D. / Ben-Shem, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structural basis for intramembrane proteolysis by rhomboid serine proteases. Authors: Ben-Shem, A. / Fass, D. / Bibi, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2irv.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2irv.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 2irv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/2irv ftp://data.pdbj.org/pub/pdb/validation_reports/ir/2irv | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 20556.393 Da / Num. of mol.: 2 / Fragment: protease core, residues 92-273 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glpG / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P09391 #4: Sugar | ChemComp-LMT / | |
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-Non-polymers , 4 types, 102 molecules
#2: Chemical | ChemComp-LDA / #3: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-PGV / ( #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 30% PEG 400, 200 mM CaCl2 in reservoir, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 17028 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Redundancy: 3 % / Rsym value: 0.081 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.411 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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