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- PDB-8izj: Crystal structure of Escherichia coli Adenine Phosphoribosyltrans... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8izj | ||||||
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Title | Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with AMP | ||||||
![]() | Adenine phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / Substrate / Nucleotide Metabolism / Salvage Pathway | ||||||
Function / homology | ![]() adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / magnesium ion binding / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yadav, P. / Kushwaha, G.S. / Bhavesh, N.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with AMP Authors: Yadav, P. / Kushwaha, G.S. / Bhavesh, N.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 71.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20163.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69503, adenine phosphoribosyltransferase |
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-Non-polymers , 5 types, 450 molecules ![](data/chem/img/AMP.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-PO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 MM TRIS-HCL PH 8.0, 20 % PEG 4000, 0.2 M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 16, 2022 / Details: KB mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→45.59 Å / Num. obs: 42857 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.041 / Rrim(I) all: 0.097 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.612 / Num. unique obs: 2114 / CC1/2: 0.871 / Rpim(I) all: 0.281 / Rrim(I) all: 0.675 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.54 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→45.59 Å
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Refine LS restraints |
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