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- PDB-1gtj: Crystal structure of the thermostable serine-carboxyl type protei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gtj | ||||||
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Title | Crystal structure of the thermostable serine-carboxyl type proteinase, kumamolisin (KSCP) - complex with Ac-Ile-Ala-Phe-cho | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / SERINE-CARBOXYL TYPE PROTEINASE / THERMOSTABLE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() tripeptidyl-peptidase activity / serine-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Comellas-Bigler, M. / Fuentes-Prior, P. / Maskos, K. / Huber, R. / Oyama, H. / Uchida, K. / Dunn, B.M. / Oda, K. / Bode, W. | ||||||
![]() | ![]() Title: The 1.4 A Crystal Structure of Kumamolysin. A Thermostable Serine-Carboxyl-Type Proteinase Authors: Comellas-Bigler, M. / Fuentes-Prior, P. / Maskos, K. / Huber, R. / Oyama, H. / Uchida, K. / Dunn, B.M. / Oda, K. / Bode, W. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.7 KB | Display | ![]() |
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PDB format | ![]() | 116.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 396.8 KB | Display | ![]() |
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Full document | ![]() | 405.1 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gt9C ![]() 1gtgC ![]() 1gtlC ![]() 1ga1S C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 36317.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: BACTERIUM FOUND IN HOTSPRING WATER NEAR VOLCANOES Production host: ![]() ![]() #2: Protein/peptide | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | THE UNBOUND INHIBITOR (CHAIN 3/4) IS ACE-ILE-ALA-PHA, N-ACETYL-L- ISOLEUCYL-N-[(2S)-1-OXO-3- ...THE UNBOUND INHIBITOR (CHAIN 3/4) IS ACE-ILE-ALA-PHA, N-ACETYL-L- ISOLEUCYL-N-[(2S)-1-OXO-3-PHENYLPROP | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.64 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 100 MM SODIUM ACETATE PH 4.5, 400 MM AMMONIUM SULPHATE | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→24.87 Å / Num. obs: 55526 / % possible obs: 90.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 2 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 2 / % possible all: 87.8 |
Reflection | *PLUS Highest resolution: 1.78 Å / Lowest resolution: 24.87 Å / Num. obs: 55533 / % possible obs: 97.3 % / Num. measured all: 114754 |
Reflection shell | *PLUS Highest resolution: 1.78 Å / % possible obs: 90.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GA1 Resolution: 1.75→24.87 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→24.87 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 53281 / Rfactor obs: 0.195 / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.195 / Highest resolution: 1.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |