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- PDB-3l92: Phosphopantetheine adenylyltransferase from Yersinia pestis compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l92 | ||||||
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Title | Phosphopantetheine adenylyltransferase from Yersinia pestis complexed with coenzyme A. | ||||||
![]() | Phosphopantetheine adenylyltransferase | ||||||
![]() | TRANSFERASE / structural genomics / phosphopantetheine adenylyltransferase / coenzyme A / ATP-binding / Coenzyme A biosynthesis / Nucleotide-binding / Nucleotidyltransferase / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osipiuk, J. / Maltseva, N. / Makowska-grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: X-ray crystal structure of phosphopantetheine adenylyltransferase from Yersinia pestis. Authors: Osipiuk, J. / Maltseva, N. / Makowska-grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.8 KB | Display | ![]() |
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PDB format | ![]() | 38.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3l93C ![]() 1h1tS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17948.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8ZJN9, pantetheine-phosphate adenylyltransferase |
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#2: Chemical | ChemComp-COA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.77 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1 M tri-sodium citrate, 0.1 M sodium cacodylate, 0.01 M coenzyme A, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2009 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→38.2 Å / Num. all: 24323 / Num. obs: 24323 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.33 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 3.81 / Num. unique all: 1205 / Χ2: 1.293 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1H1T Resolution: 1.89→38.2 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.142 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.38 Å2 / Biso mean: 26.902 Å2 / Biso min: 12.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→38.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.7857 Å / Origin y: 18.5394 Å / Origin z: 45.5202 Å
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Refinement TLS group |
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