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- PDB-5nqq: Rabbit Muscle L-lactate dehydrogenase in complex with NADH and ox... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nqq | ||||||
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Title | Rabbit Muscle L-lactate dehydrogenase in complex with NADH and oxaloacetate | ||||||
![]() | L-lactate dehydrogenase A chain | ||||||
![]() | OXIDOREDUCTASE / oxaloacetate | ||||||
Function / homology | ![]() L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luisi, B.F. / Olin-Sandoval, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization. Authors: Alam, M.T. / Olin-Sandoval, V. / Stincone, A. / Keller, M.A. / Zelezniak, A. / Luisi, B.F. / Ralser, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 508.6 KB | Display | ![]() |
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PDB format | ![]() | 424.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nqbC ![]() 3h3fS 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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Unit cell |
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Components
#1: Protein | Mass: 36598.547 Da / Num. of mol.: 4 / Mutation: THR 248 TO SER Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% wt/v PEG 3350, 50 mM Bis-tris propane pH 6.5 and 100 mM NaF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.872→29.42 Å / Num. obs: 220343 / % possible obs: 98.9 % / Redundancy: 6.6 % / Net I/σ(I): 14 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3H3F Resolution: 1.872→29.416 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.872→29.416 Å
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Refine LS restraints |
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LS refinement shell |
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