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Yorodumi- PDB-1x10: Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192A) from a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x10 | ||||||
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Title | Structure of Mutant Pyrrolidone Carboxyl Peptidase (E192A) from a Hyperthermophile, Pyrococcus furiosus | ||||||
Components | Pyrrolidone-carboxylate peptidase | ||||||
Keywords | HYDROLASE / Stability of Protein | ||||||
Function / homology | Function and homology information pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kaushik, J.K. / Yamagata, Y. / Ogasahara, K. / Yutani, K. | ||||||
Citation | Journal: Biochemistry / Year: 2006 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: Journal: J.Biochem.(Tokyo) / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x10.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x10.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 1x10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x10_validation.pdf.gz | 385 KB | Display | wwPDB validaton report |
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Full document | 1x10_full_validation.pdf.gz | 398.9 KB | Display | |
Data in XML | 1x10_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1x10_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/1x10 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/1x10 | HTTPS FTP |
-Related structure data
Related structure data | 1x12C 1z8tC 1z8wC 1z8xC 1ioiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22761.619 Da / Num. of mol.: 4 / Mutation: C142S, C188S, E192A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O73944, 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: 2.54 Å3/Da / Density % sol: 51.52 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2000 |
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: 62100 / Num. obs: 62100 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 15.2 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IOI Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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