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- PDB-5zs6: Dodecameric structure of a small Heat Shock Protein from Mycobact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zs6 | ||||||
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Title | Dodecameric structure of a small Heat Shock Protein from Mycobacterium marinum M: Form-2 | ||||||
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![]() | CHAPERONE / sHSP / oligomers / polydispersity | ||||||
Function / homology | ![]() response to salt stress / response to hydrogen peroxide / : / unfolded protein binding / protein folding / protein complex oligomerization / response to heat Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bhandari, S. / Suguna, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Dodecameric structure of a small heat shock protein from Mycobacterium marinum M. Authors: Bhandari, S. / Biswas, S. / Chaudhary, A. / Dutta, S. / Suguna, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.2 KB | Display | ![]() |
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PDB format | ![]() | 44.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.4 KB | Display | ![]() |
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Full document | ![]() | 474.3 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zs3C ![]() 5zulC ![]() 1gmeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AU
#1: Protein | Mass: 16535.803 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 458.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 9 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-PRO / | #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.12 % |
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Crystal grow | Temperature: 293 K / Method: microbatch Details: 0.2 M L-Proline, 0.1 M HEPES pH 7.5 and 24 % PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→64.5516366332 Å / Num. obs: 3204 / % possible obs: 100 % / Redundancy: 21.9 % / Biso Wilson estimate: 38.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.045 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.81→2.96 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 466 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GME Resolution: 2.81191345712→64.55 Å / SU ML: 0.293615717533 / Cross valid method: FREE R-VALUE / σ(F): 1.35348710975 / Phase error: 17.2988004223
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81191345712→64.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8119→2.9601 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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