+Open data
-Basic information
Entry | Database: PDB / ID: 3vld | ||||||
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Title | Crystal structure of yeast proteasome interacting protein | ||||||
Components | DNA mismatch repair protein HSM3 | ||||||
Keywords | CHAPERONE / HEAT REPEAT / RPT1 | ||||||
Function / homology | Function and homology information proteasome regulatory particle assembly / mismatch repair / protein folding chaperone / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å | ||||||
Authors | Takagi, K. / Kim, S. / Kato, K. / Tanaka, K. / Saeki, Y. / Mizushima, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural basis for specific recognition of Rpt1, an ATPase subunit of the 26S proteasome, by a proteasome-dedicated chaperone Hsm3 Authors: Takagi, K. / Kim, S. / Yukii, H. / Ueno, M. / Morishita, R. / Endo, Y. / Kato, K. / Tanaka, K. / Saeki, Y. / Mizushima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vld.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vld.ent.gz | 168 KB | Display | PDB format |
PDBx/mmJSON format | 3vld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vld_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 3vld_full_validation.pdf.gz | 460.5 KB | Display | |
Data in XML | 3vld_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 3vld_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/3vld ftp://data.pdbj.org/pub/pdb/validation_reports/vl/3vld | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 58241.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: HSM3, YBR1740, YBR272C / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P38348 #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: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 8% PEG 3000, 0.2M potassium phosphate, 0.1M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97916, 0.979475, 0.96424 | ||||||||||||
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Feb 16, 2009 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→76.47 Å / Num. obs: 66549 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 16.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 22 | ||||||||||||
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.9 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.05→51.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.064 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.007 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→51.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.049→2.102 Å / Total num. of bins used: 20
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