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Yorodumi- PDB-3vqm: Small heat shock protein hsp14.0 of C-terminal deletion variant w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vqm | ||||||
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Title | Small heat shock protein hsp14.0 of C-terminal deletion variant with C-terminal peptide | ||||||
Components |
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Keywords | CHAPERONE / alpha-crystallin domain | ||||||
Function / homology | Function and homology information : / Immunoglobulin-like - #790 / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Hanazono, Y. / Takeda, K. / Miki, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Structural studies on the oligomeric transition of a small heat shock protein, StHsp14.0 Authors: Hanazono, Y. / Takeda, K. / 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 | 3vqm.cif.gz | 303 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vqm.ent.gz | 247.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/3vqm ftp://data.pdbj.org/pub/pdb/validation_reports/vq/3vqm | HTTPS FTP |
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-Related structure data
Related structure data | 3vqkC 3vqlC 3aabS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 13235.255 Da / Num. of mol.: 14 / Mutation: deletion of 8 C-terminal residues Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: hsp14.0, ST1653 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q970D9 #2: Protein/peptide | Mass: 601.755 Da / Num. of mol.: 9 / Source method: obtained synthetically Details: This sequence is synthesized by the Fmoc solid phase method References: UniProt: Q970D9 #3: Water | ChemComp-HOH / | Sequence details | CHAIN A-N ARE DELETION OF EIGHT C-TERMINAL RESIDUES | |
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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: 2.69 Å3/Da / Density % sol: 54.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50 mM ammonium sulfate, 2.0% PEG8000, 15% glycerol, pH 8.0, 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: RAYONIX MX-225 / Detector: CCD / Date: Apr 20, 2011 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 65216 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.117 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3085 / Rsym value: 0.396 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AAB Resolution: 2.55→42.32 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 6700858.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3269 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→42.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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