+Open data
-Basic information
Entry | Database: PDB / ID: 3w1z | ||||||
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Title | Heat shock protein 16.0 from Schizosaccharomyces pombe | ||||||
Components | Heat shock protein 16 | ||||||
Keywords | CHAPERONE / alpha-crystallin domain / small heat shock protein | ||||||
Function / homology | Function and homology information protein aggregate center / cellular response to misfolded protein / cellular response to unfolded protein / chaperone-mediated protein folding / unfolded protein binding / cellular response to heat / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Hanazono, Y. / Takeda, K. / Akiyama, N. / Aikawa, Y. / Miki, K. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Nonequivalence Observed for the 16-Meric Structure of a Small Heat Shock Protein, SpHsp16.0, from Schizosaccharomyces pombe Authors: Hanazono, Y. / Takeda, K. / Oka, T. / Abe, T. / Tomonari, T. / Akiyama, N. / Aikawa, Y. / Yohda, M. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w1z.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w1z.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 3w1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w1z_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 3w1z_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | 3w1z_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 3w1z_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/3w1z ftp://data.pdbj.org/pub/pdb/validation_reports/w1/3w1z | HTTPS FTP |
-Related structure data
Related structure data | 1gmeS 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: 15987.883 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / Gene: hsp16 / Production host: Escherichia coli (E. coli) / References: UniProt: O14368 #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: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 15% PEGMME550, 100mM sodium chloride, 100mM Bicine buffer, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 22653 / % possible obs: 97.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 40.13 Å2 / Rsym value: 0.043 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.254 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GME Resolution: 2.401→44.834 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.7417 / SU ML: 0.41 / σ(F): 0 / Phase error: 31.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.45 Å2 / Biso mean: 51.4625 Å2 / Biso min: 10.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.401→44.834 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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