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Yorodumi- PDB-3bf0: Crystal structure of Escherichia coli Signal peptide peptidase (S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bf0 | ||||||
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Title | Crystal structure of Escherichia coli Signal peptide peptidase (SppA), Native crystals | ||||||
Components | Protease 4 | ||||||
Keywords | HYDROLASE / protease / bacterial / Inner membrane / Membrane / Transmembrane / SER/LYS Protease | ||||||
Function / homology | Function and homology information signal peptide processing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / endopeptidase activity / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å | ||||||
Authors | Paetzel, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structure of a bacterial signal Peptide peptidase. Authors: Kim, A.C. / Oliver, D.C. / Paetzel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bf0.cif.gz | 371.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bf0.ent.gz | 299.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/3bf0 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/3bf0 | HTTPS FTP |
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-Related 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: 63919.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sppA / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P08395, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: 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: 2.76 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG3350, pH 7.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97925 Å |
Detector | Type: ADSC / Detector: CCD / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 86579 / Num. obs: 86579 / % possible obs: 96.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 6 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7232 / Rsym value: 0.32 / % possible all: 80.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.851 / SU B: 9.664 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.457 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.947 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.618 Å / Total num. of bins used: 20
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