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Yorodumi- PDB-1aug: CRYSTAL STRUCTURE OF THE PYROGLUTAMYL PEPTIDASE I FROM BACILLUS A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aug | ||||||
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Title | CRYSTAL STRUCTURE OF THE PYROGLUTAMYL PEPTIDASE I FROM BACILLUS AMYLOLIQUEFACIENS | ||||||
Components | PYROGLUTAMYL PEPTIDASE-1Pyroglutamyl-peptidase I | ||||||
Keywords | THIOL PROTEASE / PYROGLUTAMYL PEPTIDASE / CYSTEINE PROTEINASE / BACILLUS AMYLOLIQUEFACIENS / HYDROLASE | ||||||
Function / homology | Function and homology information pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2 Å | ||||||
Authors | Odagaki, Y. / Hayashi, A. / Okada, K. / Hirotsu, K. / Kabashima, T. / Ito, K. / Yoshimoto, T. / Tsuru, D. / Sato, M. / Clardy, J. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: The crystal structure of pyroglutamyl peptidase I from Bacillus amyloliquefaciens reveals a new structure for a cysteine protease. Authors: Odagaki, Y. / Hayashi, A. / Okada, K. / Hirotsu, K. / Kabashima, T. / Ito, K. / Yoshimoto, T. / Tsuru, D. / Sato, M. / Clardy, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aug.cif.gz | 202.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aug.ent.gz | 160.8 KB | Display | PDB format |
PDBx/mmJSON format | 1aug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/1aug ftp://data.pdbj.org/pub/pdb/validation_reports/au/1aug | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23315.551 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: PBPG 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P46107, pyroglutamyl-peptidase I #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Feb 1, 1996 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→30 Å / Num. obs: 50037 / % possible obs: 76.8 % / Observed criterion σ(I): 2 / Redundancy: 2.43 % / Rsym value: 0.06 / Net I/σ(I): 19.82 |
Reflection shell | Resolution: 1.93→2.02 Å / Redundancy: 1.13 % / Mean I/σ(I) obs: 4.09 / Rsym value: 0.261 / % possible all: 15.1 |
Reflection | *PLUS % possible obs: 84.4 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 16.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 83443 / Rfactor obs: 0.216 / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2685 |