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- PDB-5dm5: Crystal structure of the hexameric thioesterase y2039 from Yersin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dm5 | ||||||
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Title | Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis | ||||||
![]() | Putative acyl-CoA thioester hydrolase | ||||||
![]() | HYDROLASE / thioesterase / hot-dog fold | ||||||
Function / homology | ![]() thiolester hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Swarbrick, C.M.D. / Forwood, J.K. | ||||||
![]() | ![]() Title: Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis Authors: Swarbrick, C.M.D. / Forwood, J.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 | ![]() | 146.6 KB | Display | ![]() |
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PDB format | ![]() | 116.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.4 KB | Display | ![]() |
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Full document | ![]() | 523.7 KB | Display | |
Data in XML | ![]() | 30 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yliS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16147.383 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7CIM6, UniProt: A0A5P8YGN6*PLUS, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.27 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 800 mM potassium sodium tartrate tetrahydrate, 120 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→34.878 Å / Num. obs: 25310 / % possible obs: 94.68 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YLI Resolution: 2.7→34.878 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.51 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→34.878 Å
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Refine LS restraints |
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LS refinement shell |
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