+Open data
-Basic information
Entry | Database: PDB / ID: 3b44 | ||||||
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Title | Crystal structure of GlpG W136A mutant | ||||||
Components | glpGRhomboid protease | ||||||
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: 1.7 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 | 3b44.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b44.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 3b44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/3b44 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/3b44 | HTTPS FTP |
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-Related structure data
Related structure data | 3b45C 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: 20228.002 Da / Num. of mol.: 1 / Fragment: core TM fragment, residues 91-270 / Mutation: W136A 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: 3.72 Å3/Da / Density % sol: 66.9 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 3.5M NH4Cl, 100mM Tris-HCl pH 8.5, 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: 1.7→40 Å / Num. all: 33222 / Num. obs: 33056 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 4.1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Starting model: 2IC8 Resolution: 1.7→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Displacement parameters | Biso mean: 28.05 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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