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- PDB-1z8w: Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192I) from a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1z8w | ||||||
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Title | Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192I) from a Hyperthermophile, Pyrococcus furiosus | ||||||
![]() | Pyrrolidone-carboxylate peptidase | ||||||
![]() | HYDROLASE / Protein Stability | ||||||
Function / homology | ![]() pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kaushik, J.K. / Yamagata, Y. / Ogasahara, K. / Yutani, K. | ||||||
![]() | ![]() Title: Completely buried, non-ion-paired glutamic acid contributes favorably to the conformational stability of pyrrolidone carboxyl peptidases from hyperthermophiles. Authors: Kaushik, J.K. / Iimura, S. / Ogasahara, K. / Yamagata, Y. / Segawa, S. / Yutani, K. #1: ![]() Title: X-ray crystalline structures of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus, and its cys-free mutant Authors: Tanaka, H. / Chinami, M. / Mizushima, T. / Ogasahara, K. / Ota, M. / Tsukihara, T. / Yutani, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184 KB | Display | ![]() |
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PDB format | ![]() | 147.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383 KB | Display | ![]() |
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Full document | ![]() | 399.7 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1x10SC ![]() 1x12C ![]() 1z8tC ![]() 1z8xC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22803.699 Da / Num. of mol.: 4 / Mutation: C142,188S E192I 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: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 60478 / Num. obs: 60478 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 36.8 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 19.4 / % possible all: 69.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1X10 Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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