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Yorodumi- PDB-3bez: Crystal structure of Escherichia coli Signal peptide peptidase (S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bez | ||||||
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Title | Crystal structure of Escherichia coli Signal peptide peptidase (SppA), SeMet crystals | ||||||
Components | Protease 4 | ||||||
Keywords | HYDROLASE / protease / bacterial / Inner membrane / Membrane / Transmembrane | ||||||
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 / SAD / Resolution: 2.76 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 | 3bez.cif.gz | 374.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bez.ent.gz | 313.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/3bez ftp://data.pdbj.org/pub/pdb/validation_reports/be/3bez | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
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-Components
#1: Protein | Mass: 64623.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / 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: 2.68 Å3/Da / Density % sol: 54.03 % |
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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: 2.76→46.9 Å / Num. obs: 69169 / % possible obs: 97.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.178 / Rsym value: 0.178 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.76→2.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5523 / Rsym value: 0.33 / % possible all: 78 |
-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.76→46.63 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.873 / SU B: 12.425 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.961 / ESU R Free: 0.348 / 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: 25.373 Å2
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Refinement step | Cycle: LAST / Resolution: 2.76→46.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.76→2.828 Å / Total num. of bins used: 20
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