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Yorodumi- PDB-7yy5: Crystal structure of Mycobacterium abscessus Phosphopantetheine a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yy5 | ||||||
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Title | Crystal structure of Mycobacterium abscessus Phosphopantetheine adenylyltransferase in complex with Fragment 9 | ||||||
Components | Phosphopantetheine adenylyltransferase | ||||||
Keywords | TRANSFERASE / CoaD / PPAT / nucleotidyltransferase | ||||||
Function / homology | Function and homology information pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacteroides abscessus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.499 Å | ||||||
Authors | Thomas, S.E. / Coyne, A.G. / Blundell, T.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Front Mol Biosci / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yy5.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yy5.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 7yy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yy5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7yy5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7yy5_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 7yy5_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/7yy5 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/7yy5 | HTTPS FTP |
-Related structure data
Related structure data | 7ywmC 7yxzC 7yy0C 7yy1C 7yy2C 7yy3C 7yy4C 7yy6C 7yy7C 7yy8C 7yy9C 7yyaC 7yybC 7yycC 5o06S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Mycobacteroides abscessus (bacteria) / Gene: coaD, MAB_3259c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B1MDL6, pantetheine-phosphate adenylyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.48 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å | ||||||||||||||||||||||||||||||
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: 1.499→64.84 Å / Num. obs: 90979 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.05 / Rrim(I) all: 0.14 / Net I/σ(I): 9.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5O06 Resolution: 1.499→64.836 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.69 / 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: 108.79 Å2 / Biso mean: 28.8697 Å2 / Biso min: 10.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.499→64.836 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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Refinement TLS params. | Method: refined / Origin x: -12.634 Å / Origin y: -21.4206 Å / Origin z: -26.0912 Å
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Refinement TLS group |
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