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- PDB-5o0d: Crystal structure of Phosphopantetheine adenylyltransferase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o0d | ||||||
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Title | Crystal structure of Phosphopantetheine adenylyltransferase from Mycobacterium abcessus in complex with 3-Phenoxymandelic acid (Fragment 4) | ||||||
![]() | Phosphopantetheine adenylyltransferase | ||||||
![]() | TRANSFERASE / Coenzyme A Biosynthesis | ||||||
Function / homology | ![]() pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomas, S.E. / Kim, S.Y. / Mendes, V. / Blaszczyk, M. / Blundell, T.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew. Authors: Thomas, S.E. / Mendes, V. / Kim, S.Y. / Malhotra, S. / Ochoa-Montano, B. / Blaszczyk, M. / Blundell, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112 KB | Display | ![]() |
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PDB format | ![]() | 85.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5o06SC ![]() 5o08C ![]() 5o0aC ![]() 5o0bC ![]() 5o0cC ![]() 5o0fC ![]() 5o0hC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 17476.887 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: coaD, MAB_3259c / Production host: ![]() ![]() References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 200mM Sodium Bromide 20-25% PEG 3350 0.1M Bis-Tris propane PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.539→119.14 Å / Num. obs: 84215 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 21.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.056 / Rrim(I) all: 0.156 / Net I/σ(I): 9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5O06 Resolution: 1.539→62.596 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.05 Å2 / Biso mean: 28.5212 Å2 / Biso min: 13.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.539→62.596 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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