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Open data
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Basic information
Entry | Database: PDB / ID: 1k32 | ||||||
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Title | Crystal structure of the tricorn protease | ||||||
![]() | tricorn protease | ||||||
![]() | HYDROLASE / protein degradation / substrate gating / serine protease / beta propeller / proteasome | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Brandstetter, H. / Kim, J.-S. / Groll, M. / Huber, R. | ||||||
![]() | ![]() Title: Crystal structure of the tricorn protease reveals a protein disassembly line. Authors: Brandstetter, H. / Kim, J.S. / Groll, M. / Huber, R. | ||||||
History |
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Remark 600 | HETEROGEN HOH 2001-2399 ARE ASSOCIATED WITH CHAIN A. HOH 3001-3399 ARE ASSOCIATED WITH CHAIN B. HOH ...HETEROGEN HOH 2001-2399 ARE ASSOCIATED WITH CHAIN A. HOH 3001-3399 ARE ASSOCIATED WITH CHAIN B. HOH 4001-4399 ARE ASSOCIATED WITH CHAIN C. HOH 5001-5399 ARE ASSOCIATED WITH CHAIN D. HOH 6001-6399 ARE ASSOCIATED WITH CHAIN E. HOH 7001-7399 ARE ASSOCIATED WITH CHAIN F. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1004.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Unit cell |
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Details | homohexamer following 3-2 symmetry, completely contained in the coordinate file |
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Components
#1: Protein | Mass: 118680.055 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P96086, 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: 2.54 Å3/Da / Density % sol: 51.56 % | ||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% isopropanol, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||
Crystal | *PLUS Density % sol: 51 % | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||
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: Dec 10, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 475881 / Num. obs: 394093 / % possible obs: 82.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 1.9 / Num. unique all: 394093 / Rsym value: 0.313 / % possible all: 68.1 |
Reflection | *PLUS Rmerge(I) obs: 0.208 |
Reflection shell | *PLUS Rmerge(I) obs: 0.313 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() ![]() Cross valid method: direct space free density correlation reciprocal free R σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.74 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.04 Å
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Refinement | *PLUS Rfactor obs: 0.248 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.248 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.323 / Rfactor Rwork: 0.289 |