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Open data
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Basic information
Entry | Database: PDB / ID: 3l93 | ||||||
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Title | Phosphopantetheine adenylyltransferase from Yersinia pestis. | ||||||
![]() | Phosphopantetheine adenylyltransferase | ||||||
![]() | TRANSFERASE / structural genomics / phosphopantetheine adenylyltransferase / 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 | ![]() | 48.8 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
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Full document | ![]() | 441 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3l92SC 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
#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-FMT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.63 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 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: 2.16→32.3 Å / Num. all: 16233 / Num. obs: 16233 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.875 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.17→2.21 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.88 / Num. unique all: 807 / Χ2: 1.484 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3L92 Resolution: 2.16→32.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.388 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.146 / ESU R Free: 0.139 / 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: 67.86 Å2 / Biso mean: 34.293 Å2 / Biso min: 19.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→32.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.161→2.217 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 4.7938 Å / Origin y: 19.034 Å / Origin z: 45.1136 Å
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Refinement TLS group |
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