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- PDB-1kn9: CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kn9 | ||||||
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Title | CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM. | ||||||
![]() | Signal peptidase I | ||||||
![]() | HYDROLASE / serine protease / Lysine general base / membrane protein / mostly beta-fold | ||||||
Function / homology | ![]() signal peptidase I / thylakoid membrane organization / signal peptide processing / protein processing / peptidase activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Paetzel, M. / Dalbey, R.E. / Strynadka, N.C.J. | ||||||
![]() | ![]() Title: Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism Authors: Paetzel, M. / Dalbey, R.E. / Strynadka, N.C.J. #1: ![]() Title: Crystal structure of a bacterial signal peptidase in complex with a beta-lactam inhibitor. Authors: Paetzel, M. / Dalbey, R.E. / Strynadka, N.C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.6 KB | Display | ![]() |
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PDB format | ![]() | 148.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 391.8 KB | Display | ![]() |
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Full document | ![]() | 410.2 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b12S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27966.658 Da / Num. of mol.: 4 / Fragment: Residues 76-323, plus initiating methionine Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.2 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: ammonium dihydrogen phosphate, sodium citrate, Triton X-100, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 8, 2000 / Details: mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 49984 / Num. obs: 49984 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 5.8 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 277201 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B12 Resolution: 2.4→40.05 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2760295.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.3593 Å2 / ksol: 0.348658 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→40.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 45.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.353 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.284 |