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- PDB-1iu8: The X-ray Crystal Structure of Pyrrolidone-Carboxylate Peptidase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1iu8 | ||||||
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Title | The X-ray Crystal Structure of Pyrrolidone-Carboxylate Peptidase from Hyperthermophilic Archaeon Pyrococcus horikoshii | ||||||
![]() | Pyrrolidone-carboxylate peptidase | ||||||
![]() | HYDROLASE / Thiol protease | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sokabe, M. / Kawamura, T. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
![]() | ![]() Title: The X-ray crystal structure of pyrrolidone-carboxylate peptidase from hyperthermophilic archaea Pyrococcus horikoshii Authors: Sokabe, M. / Kawamura, T. / Sakai, N. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.5 KB | Display | ![]() |
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PDB format | ![]() | 77.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 436.4 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iofS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22667.129 Da / Num. of mol.: 2 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: 2.3 Å3/Da / Density % sol: 53.5 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: MPD, Magnesium Chlolide, Imidazole, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / PH range low: 9 / PH range high: 7.4 | |||||||||||||||||||||||||||||||||||
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 23, 2001 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→23.6 Å / Num. all: 54101 / Num. obs: 54101 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.211 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.6→1.686 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3 / Num. unique all: 7861 / Rsym value: 0.231 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.6 Å / % possible obs: 100 % / Num. measured all: 207328 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IOF Resolution: 1.6→20 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: throughout / Bsol: 49.57 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.3 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2689 |