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- PDB-1iof: X-RAY CRYSTALLINE STRUCTURES OF PYRROLIDONE CARBOXYL PEPTIDASE FR... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iof | ||||||
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Title | X-RAY CRYSTALLINE STRUCTURES OF PYRROLIDONE CARBOXYL PEPTIDASE FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS, AND ITS CYS-FREE MUTANT | ||||||
![]() | PYRROLIDONE CARBOXYL PEPTIDASE | ||||||
![]() | HYDROLASE / PGP-I / PYROGLUTAMYL-PEPTIDASE I / PCP / protease / Pyrococcus furiosus / Archaea | ||||||
Function / homology | ![]() pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tanaka, H. / Chinami, M. / Ota, M. / Tsukihara, T. / Yutani, K. | ||||||
![]() | ![]() 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 | ![]() | 169.5 KB | Display | ![]() |
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PDB format | ![]() | 136.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390 KB | Display | ![]() |
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Full document | ![]() | 411.8 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ioiC ![]() 1augS 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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Unit cell |
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Details | The biological assembly is a tetramer. |
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Components
#1: Protein | Mass: 22851.783 Da / Num. of mol.: 4 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: 2.61 Å3/Da / Density % sol: 52.85 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, sodium acetate, EDTA, DTE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 5, 1996 / Details: graphite-monochromater |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→200 Å / Num. all: 350572 / Num. obs: 169460 / % possible obs: 91.5 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4137 / % possible all: 69.9 |
Reflection shell | *PLUS % possible obs: 69.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AUG Resolution: 2.2→10 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Software | *PLUS Name: 'X-PLOR' / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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