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- PDB-7yy3: Crystal structure of Mycobacterium abscessus Phosphopantetheine a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yy3 | ||||||
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Title | Crystal structure of Mycobacterium abscessus Phosphopantetheine adenylyltransferase in complex with Fragment 7 | ||||||
![]() | Phosphopantetheine adenylyltransferase | ||||||
![]() | TRANSFERASE / CoaD / PPAT / nucleotidyltransferase | ||||||
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. / Coyne, A.G. / Blundell, T.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Characterization of Mycobacterium abscessus Phosphopantetheine Adenylyl Transferase Ligand Interactions: Implications for Fragment-Based Drug Design. Authors: Thomas, S.E. / McCarthy, W.J. / El Bakali, J. / Brown, K.P. / Kim, S.Y. / Blaszczyk, M. / Mendes, V. / Abell, C. / Floto, R.A. / Coyne, A.G. / 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 | ![]() | 109.6 KB | Display | ![]() |
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PDB format | ![]() | 83.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ywmC ![]() 7yxzC ![]() 7yy0C ![]() 7yy1C ![]() 7yy2C ![]() 7yy4C ![]() 7yy5C ![]() 7yy6C ![]() 7yy7C ![]() 7yy8C ![]() 7yy9C ![]() 7yyaC ![]() 7yybC ![]() 7yycC ![]() 5o06S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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.) ![]() ![]() ![]() References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.61 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium bromide, 20-24 % PEG3350, 0.1 M Bis-Tris propane pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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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: 1.535→64.95 Å / Num. obs: 85029 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.033 / Rrim(I) all: 0.094 / Net I/σ(I): 13 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: ![]() |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5O06 Resolution: 1.535→57.053 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.6 Å2 / Biso mean: 30.3146 Å2 / Biso min: 14.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.535→57.053 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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