+Open data
-Basic information
Entry | Database: PDB / ID: 1j2p | ||||||
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Title | alpha-ring from the proteasome from archaeoglobus fulgidus | ||||||
Components | Proteasome alpha subunit | ||||||
Keywords | HYDROLASE / proteasome / alpha-ring | ||||||
Function / homology | Function and homology information proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Groll, M. / Brandstetter, H. / Bartunik, H. / Bourenkow, G. / Huber, R. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 Title: Investigations on the Maturation and Regulation of Archaebacterial Proteasomes Authors: Groll, M. / Brandstetter, H. / Bartunik, H. / Bourenkow, G. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j2p.cif.gz | 349.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j2p.ent.gz | 285.8 KB | Display | PDB format |
PDBx/mmJSON format | 1j2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/1j2p ftp://data.pdbj.org/pub/pdb/validation_reports/j2/1j2p | HTTPS FTP |
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-Related 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: 27694.027 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) References: UniProt: O29760, proteasome endopeptidase complex #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: 2.35 Å3/Da / Density % sol: 47.71 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 3M 1,6-Hexandiol, 85mM Magnesiumchlorid, 100mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / pH: 4.6 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 4, 2000 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 1248529 / Num. obs: 67959 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 20.2 Å2 |
Reflection shell | Resolution: 2.58→2.63 Å / % possible all: 99 |
Reflection | *PLUS Highest resolution: 2.45 Å / Lowest resolution: 20 Å / Num. measured all: 1248529 / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS Rmerge(I) obs: 0.367 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: proteasome from thermoplasma acidophilum Resolution: 2.6→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2800328.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.3397 Å2 / ksol: 0.297951 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.45 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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