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Yorodumi- PDB-1g2i: CRYSTAL STRUCTURE OF A NOVEL INTRACELLULAR PROTEASE FROM PYROCOCC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2i | ||||||
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Title | CRYSTAL STRUCTURE OF A NOVEL INTRACELLULAR PROTEASE FROM PYROCOCCUS HORIKOSHII AT 2 A RESOLUTION | ||||||
Components | PROTEASE I | ||||||
Keywords | HYDROLASE / intracellular protease / ATP-independent intracellular protease / protease / catalytical triad / PfpI / cysteine protease / nucleophile elbow / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information protein deglycase / protein deglycase activity / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Du, X. / Choi, I.-G. / Kim, R. / Jancarik, J. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-A resolution. Authors: Du, X. / Choi, I.G. / Kim, R. / Wang, W. / Jancarik, J. / Yokota, H. / Kim, S.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2i.cif.gz | 111.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2i.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 1g2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g2i_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 1g2i_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 1g2i_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1g2i_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2i ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2i | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The other three monomers of the hexameric complex may be generated by:y,x,-z-1 |
-Components
#1: Protein | Mass: 18837.998 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1704 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)/SJS1244 / References: UniProt: O59413, Hydrolases; Glycosylases #2: Chemical | ChemComp-SO4 / | #3: 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: 4.43 Å3/Da / Density % sol: 72.27 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Tris-HCl, EDTA, trisodium citrate dihydrate, potassium tartarate tetrahydrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 195 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97938,0.9796,0.9686 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 27, 1999 | ||||||||||||
Radiation | Monochromator: Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. all: 131170 / Num. obs: 129727 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.9 | ||||||||||||
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.7 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3763370.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.4 Å2 / ksol: 0.393 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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