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- PDB-6a75: Crystal structure of the complex of Phosphopantetheine adenylyltr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a75 | ||||||
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Title | Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephospho Coenzyme A at 2.75 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: Crystal structure of the complex of Phosphopantetheine adenylyltransferase from Acinetobacter baumannii with Dephospho Coenzyme A at 2.75 A resolution Authors: Singh, P.K. / Gupta, A. / Kaur, 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 | ![]() | 51.1 KB | Display | ![]() |
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PDB format | ![]() | 36.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5yh7S S: Starting model for refinement |
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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
-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.) ![]() Strain: ACICU / Gene: coaD, ACICU_00798 / Production host: ![]() ![]() References: UniProt: B2HUN5, pantetheine-phosphate adenylyltransferase |
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-Non-polymers , 5 types, 45 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/COD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-COD / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.75 Å3/Da / Density % sol: 78.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1M LITHIUM SULPHATE, 0.5M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6 PH range: 4-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 19, 2018 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→48.5 Å / Num. obs: 11866 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 63.5 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 15.04 |
Reflection shell | Resolution: 2.75→2.82 Å / Redundancy: 15 % / Mean I/σ(I) obs: 8.05 / Num. unique obs: 810 / CC1/2: 0.98 / Rrim(I) all: 0.47 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5yh7 Resolution: 2.75→48.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.824 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.224 / 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: 56.885 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→48.5 Å
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Refine LS restraints |
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