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- PDB-5szv: Novel Structural Insights into GDP-Mediated Regulation of Acyl-Co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5szv | ||||||
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Title | Novel Structural Insights into GDP-Mediated Regulation of Acyl-CoA Thioesterases | ||||||
![]() | Acyl-CoA hydrolase | ||||||
![]() | HYDROLASE / Thioesterase / Nisseria meningitidis / 4HBT / Acyl-CoA thioesterase / Coenzyme A / GDP | ||||||
Function / homology | ![]() palmitic acid biosynthetic process / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Khandokar, Y.B. / Srivastava, P. / Forwood, J.K. | ||||||
![]() | ![]() Title: Structural insights into GDP-mediated regulation of a bacterial acyl-CoA thioesterase. Authors: Khandokar, Y.B. / Srivastava, P. / Cowieson, N. / Sarker, S. / Aragao, D. / Das, S. / Smith, K.M. / Raidal, S.R. / 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 | ![]() | 240.4 KB | Display | ![]() |
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PDB format | ![]() | 198.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5szuC ![]() 5szyC ![]() 5szzC ![]() 5t02C ![]() 5v3aC ![]() 4ienS C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17984.541 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: ERS514298_01532, ERS514410_00397, ERS514534_01643, ERS514708_01580, ERS514851_00814 Production host: ![]() ![]() References: UniProt: A0A0Y5D4F5, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.91 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris pH 8.5 and 2 M ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015 |
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→35.88 Å / Num. obs: 79249 / % possible obs: 100 % / Redundancy: 24.2 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 17.22 |
Reflection shell | Resolution: 2→2.071 Å / Redundancy: 24.5 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 3.01 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4IEN Resolution: 2→35.88 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→35.88 Å
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Refine LS restraints |
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LS refinement shell |
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