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- PDB-5hru: Crystal structure of Plasmodium vivax LDH in complex with a DNA a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hru | |||||||||
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Title | Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1 | |||||||||
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![]() | OXIDOREDUCTASE/DNA / DNA aptamer / Plasmodium LDH / malaria / DNA structural element / OXIDOREDUCTASE-DNA complex | |||||||||
Function / homology | ![]() lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / nucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Choi, S.J. / Ban, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition Authors: Choi, S.J. / Ban, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.4 KB | Display | ![]() |
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PDB format | ![]() | 225.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hs4C ![]() 5htoC ![]() 2a92S C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37659.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LDH / Plasmid: pET28a / Production host: ![]() ![]() #2: DNA chain | | Mass: 9944.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 293.19 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG-20K, NDSB-195, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.71→25 Å / Num. obs: 82531 / % possible obs: 99.8 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.103 / Net I/av σ(I): 80.476 / Net I/σ(I): 15 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2A92 Resolution: 1.71→24.96 Å
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Displacement parameters | Biso max: 99.02 Å2 / Biso mean: 24.2256 Å2 / Biso min: 11.36 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→24.96 Å
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LS refinement shell | Resolution: 1.712→1.773 Å
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