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- PDB-4i5w: Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP -
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Open data
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Basic information
Entry | Database: PDB / ID: 4i5w | ||||||
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Title | Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP | ||||||
![]() | 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, Y.L. / Hou, W.T. / Chen, Y. / Zhou, C.Z. | ||||||
![]() | ![]() Title: Structures of yeast Apa2 reveal catalytic insights into a canonical AP4A phosphorylase of the histidine triad superfamily Authors: Hou, W.T. / Li, W.Z. / Chen, Y. / Jiang, Y.L. / Zhou, C.Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.5 KB | Display | ![]() |
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PDB format | ![]() | 103.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37902.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: S288c / Gene: APA2, YDR530C, D9719.33 / Plasmid: pET-28a / Production host: ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / | ![]() #3: Chemical | ChemComp-AMP / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.4 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18% PEG 2K, 0.1M MES, 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 315r / Detector: CCD / Date: Oct 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.793→50 Å / Num. obs: 15784 / % possible obs: 94.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 60.1 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.6 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.638 Å2 / ksol: 0.269 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.793→43.559 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: 11
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