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Yorodumi- PDB-5hru: Crystal structure of Plasmodium vivax LDH in complex with a DNA a... -
+Open data
-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 | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/DNA / DNA aptamer / Plasmodium LDH / malaria / DNA structural element / OXIDOREDUCTASE-DNA complex | |||||||||
Function / homology | Function and homology information carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | |||||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) Phylica emirnensis (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | |||||||||
Authors | Choi, S.J. / Ban, C. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Sci Rep / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hru.cif.gz | 286.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hru.ent.gz | 225.6 KB | Display | PDB format |
PDBx/mmJSON format | 5hru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/5hru ftp://data.pdbj.org/pub/pdb/validation_reports/hr/5hru | HTTPS FTP |
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-Related structure data
Related structure data | 5hs4C 5htoC 2a92S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Plasmodium vivax (malaria parasite P. vivax) Gene: LDH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q4PRK9, L-lactate dehydrogenase #2: DNA chain | | Mass: 9944.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Phylica emirnensis (plant) #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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