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- PDB-6vdj: Crystal structure of ancestral apicomplexan lactate dehydrogenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vdj | ||||||
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Title | Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate and NADH4. | ||||||
![]() | lactate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Nucleotide Binding / Rossman Fold / Ancestral Reconstruction | ||||||
Function / homology | L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-TXD![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Theobald, D.L. / Wirth, J.D. / Classen, S. / Perlmutter, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase Authors: Theobald, D.L. / Wirth, J.D. / Classen, S. / Perlmutter, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 269.7 KB | Display | ![]() |
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PDB format | ![]() | 177.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 365.4 KB | Display | ![]() |
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Full document | ![]() | 368.2 KB | Display | |
Data in XML | ![]() | 2.4 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vdhC ![]() 6vdiC ![]() 4plgS S: Starting model for refinement C: citing same article ( |
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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: 35905.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Ancestral apicomplexan lactate dehydrogenase with sulfate and NADH4 bound Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-TXD / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20mg/mL protein, 2mM NADH4; well solution: 9% v/v 2-Propanol, 1.4M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2019 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115866 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→48.79 Å / Num. obs: 146503 / % possible obs: 96.4 % / Redundancy: 8.84 % / Biso Wilson estimate: 48.39 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.16 / Χ2: 0.89 / Net I/σ(I): 5.02 |
Reflection shell | Resolution: 1.43→1.52 Å / Redundancy: 2.94 % / Num. unique obs: 105617 / CC1/2: 0.009 / Rrim(I) all: 383.6 / % possible all: 76.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PLG Resolution: 2→48.79 Å / SU ML: 0.3709 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.6369 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.79 Å
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Refine LS restraints |
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LS refinement shell |
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