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- PDB-8i8p: Crystal structure of the complex of phosphopantetheine adenylyltr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i8p | |||||||||
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Title | Crystal structure of the complex of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephosphocoenzyme-A at 2.19 A resolution. | |||||||||
![]() | Phosphopantetheine adenylyltransferase | |||||||||
![]() | TRANSFERASE / coaD / PPAT / 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 | ![]() ![]() ![]() | |||||||||
![]() | Ahmad, N. / Viswanathan, V. / Gupta, A. / Sharma, P. / Sharma, S. / Singh, T.P. | |||||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of the complex of phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephosphocoenzyme-A at 2.19 A resolution. Authors: Ahmad, N. / Viswanathan, V. / Gupta, A. / Sharma, P. / 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 | ![]() | 53.5 KB | Display | ![]() |
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PDB format | ![]() | 37.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18479.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: coaD, HMPREF0010_01342 Production host: ![]() ![]() References: UniProt: D0C9M9, pantetheine-phosphate adenylyltransferase |
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-Non-polymers , 5 types, 94 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/COD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-COD / | ||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.76 Å3/Da / Density % sol: 78.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1M LITHIUM SULPHATE, 2M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97199 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→125.307 Å / Num. obs: 22090 / % possible obs: 95.48 % / Redundancy: 20 % / CC1/2: 0.99 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.19→2.25 Å / Num. unique obs: 1044 / CC1/2: 0.631 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.419 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→125.307 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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