+Open data
-Basic information
Entry | Database: PDB / ID: 4h1d | ||||||
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Title | Cocrystal structure of GlpG and DFP | ||||||
Components | Rhomboid protease GlpG | ||||||
Keywords | HYDROLASE / intramembrane protease / serine protease / DFP / membrane protein | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.8975 Å | ||||||
Authors | Xue, Y. / Ha, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Large lateral movement of transmembrane helix s5 is not required for substrate access to the active site of rhomboid intramembrane protease. Authors: Xue, 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 | 4h1d.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h1d.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 4h1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/4h1d ftp://data.pdbj.org/pub/pdb/validation_reports/h1/4h1d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20214.020 Da / Num. of mol.: 1 / Fragment: UNP Residues 92-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glpG, b3424, JW5687 / Production host: Escherichia coli (E. coli) / References: UniProt: P09391, rhomboid protease |
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#2: Chemical | ChemComp-DFP / |
#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: 3.58 Å3/Da / Density % sol: 65.6 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7 Details: 0.1 M bis-tris propane 1.5 M NH4Cl, pH 7, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8975→40 Å / Num. all: 6580 / Num. obs: 6580 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8975→37.787 Å / SU ML: 0.36 / σ(F): 1.92 / Phase error: 32.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.251 Å2 / ksol: 0.296 e/Å3 | |||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8975→37.787 Å
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Refine LS restraints |
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LS refinement shell |
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