+Open data
-Basic information
Entry | Database: PDB / ID: 2h6j | ||||||
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Title | Crystal Structure of the Beta F145A Rhodococcus Proteasome | ||||||
Components |
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Keywords | HYDROLASE / 20S proteasome / half proteasome / assembly-dependent activation | ||||||
Function / homology | Function and homology information proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / modification-dependent protein catabolic process / endopeptidase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Rhodococcus erythropolis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Kwon, Y.D. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Proteasome assembly triggers a switch required for active-site maturation. Authors: Witt, S. / Kwon, Y.D. / Sharon, M. / Felderer, K. / Beuttler, M. / Robinson, C.V. / Baumeister, W. / Jap, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h6j.cif.gz | 573.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h6j.ent.gz | 453.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h6j ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h6j | HTTPS FTP |
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-Related structure data
Related structure data | 1q5rS S: Starting model for refinement |
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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: 28346.840 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: prcA 1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q53080, proteasome endopeptidase complex #2: Protein | Mass: 31122.484 Da / Num. of mol.: 7 / Mutation: F145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: prcB 1 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q53079, proteasome endopeptidase complex #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: 2.35 Å3/Da / Density % sol: 47.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16-18 % PEG 3350, 50mM Sodium Citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2004 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 66462 / % possible obs: 94.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q5R Resolution: 3.2→19.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 273660.74 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.4592 Å2 / ksol: 0.20798 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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