+Open data
-Basic information
Entry | Database: PDB / ID: 3b45 | ||||||
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Title | Crystal structure of GlpG at 1.9A resolution | ||||||
Components | glpG | ||||||
Keywords | MEMBRANE PROTEIN / intramembrane protease / integral membrane protein / serine protease / DNA-binding / Glycerol metabolism / Inner membrane / Transmembrane | ||||||
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 / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Wang, Y. / Maegawa, S. / Akiyama, Y. / Ha, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. Authors: Wang, Y. / Maegawa, S. / Akiyama, Y. / Ha, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b45.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b45.ent.gz | 38.8 KB | Display | PDB format |
PDBx/mmJSON format | 3b45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b45_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3b45_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3b45_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3b45_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/3b45 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b45 | HTTPS FTP |
-Related structure data
Related structure data | 3b44C 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20343.133 Da / Num. of mol.: 1 / Fragment: core TM fragment, residues 91-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09391 | ||
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#2: Sugar | ChemComp-BNG / #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: 3.76 Å3/Da / Density % sol: 67.28 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5M NH4Cl, 100mM Bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 24277 / Num. obs: 23768 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.2 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Starting model: 2IC8 Resolution: 1.9→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Displacement parameters | Biso mean: 35.625 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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