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Open data
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Basic information
Entry | Database: PDB / ID: 1ky9 | ||||||
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Title | Crystal Structure of DegP (HtrA) | ||||||
![]() | PROTEASE DO | ||||||
![]() | HYDROLASE / protein quality control / serine protease / trypsin / chaperone / PDZ / ATP-independent / temperature-regulated / periplasm / cage-forming protein | ||||||
Function / homology | ![]() peptidase Do / programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / response to heat / outer membrane-bounded periplasmic space ...peptidase Do / programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / response to heat / outer membrane-bounded periplasmic space / response to oxidative stress / periplasmic space / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krojer, T. / Garrido-Franco, M. / Huber, R. / Ehrmann, M. / Clausen, T. | ||||||
![]() | ![]() Title: Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine. Authors: Krojer, T. / Garrido-Franco, M. / Huber, R. / Ehrmann, M. / Clausen, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.7 KB | Display | ![]() |
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PDB format | ![]() | 119.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 504.1 KB | Display | |
Data in XML | ![]() | 34.9 KB | Display | |
Data in CIF | ![]() | 47.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Details | Hexamers of molecule A and B are entirely formed by crystal symmetry. |
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Components
#1: Protein | Mass: 47509.449 Da / Num. of mol.: 2 / Mutation: S210A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0C0V0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.94 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Isopropanol, PEG 2000 MME, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2001 | ||||||||||||
Radiation | Monochromator: Si111 or Si311 crystals, LN2 cooled / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→20 Å / Num. all: 48422 / Num. obs: 48312 / % possible obs: 97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 82 Å2 / Rsym value: 0.083 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4397 / Rsym value: 0.469 / % possible all: 92.2 | ||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.083 | ||||||||||||
Reflection shell | *PLUS % possible obs: 92.2 % / Rmerge(I) obs: 0.469 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor all: 0.229 / Rfactor obs: 0.218 / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.218 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 2 |