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- PDB-5yh7: Crystal structure of the complex of Phosphopantetheine adenylyltr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yh7 | ||||||
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Title | Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Coenzyme A at 2.0 A resolution | ||||||
![]() | Phosphopantetheine adenylyltransferase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singh, P.K. / Gupta, A. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
![]() | ![]() Title: Structural and binding studies of phosphopantetheine adenylyl transferase from Acinetobacter baumannii. Authors: Gupta, A. / Singh, P.K. / Iqbal, N. / Sharma, P. / Baraigya, H.R. / Kaur, P. / Umar, M.S. / Ahmad, F. / Sharma, A. / Owais, M. / Sharma, S. / Singh, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52 KB | Display | ![]() |
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PDB format | ![]() | 37.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5h7xC ![]() 1h1tS 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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Unit cell |
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Components
#1: Protein | Mass: 18479.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ACICU / Gene: coaD, ACICU_00798 / Production host: ![]() ![]() References: UniProt: B2HUN5, pantetheine-phosphate adenylyltransferase | ||
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#2: Chemical | ChemComp-COA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.6 Å3/Da / Density % sol: 78.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH- 5.6 PH range: 5-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2017 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2→125.24 Å / Num. obs: 24872 / % possible obs: 88.1 % / Redundancy: 8.3 % / Rsym value: 0.072 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.39 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1H1T Resolution: 2.03→125.24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.546 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.271 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→125.24 Å
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Refine LS restraints |
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