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- PDB-2a94: Structure of Plasmodium falciparum lactate dehydrogenase complexe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2a94 | |||||||||
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Title | Structure of Plasmodium falciparum lactate dehydrogenase complexed to APADH. | |||||||||
![]() | L-lactate dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / Rossmann fold | |||||||||
Function / homology | ![]() L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chaikuad, A. / Fairweather, V. / Conners, R. / Joseph-Horne, T. / Turgut-Balik, D. / Brady, R.L. | |||||||||
![]() | ![]() Title: Structure of Lactate Dehydrogenase from Plasmodium vivax: Complexes with NADH and APADH. Authors: Chaikuad, A. / Fairweather, V. / Conners, R. / Joseph-Horne, T. / Turgut-Balik, D. / Brady, R.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.3 KB | Display | ![]() |
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PDB format | ![]() | 58.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2a92C ![]() 2aa3C ![]() 1t2cS 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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Details | Biological unit is a tetramer |
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Components
#1: Protein | Mass: 34846.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LDH / Plasmid: pKK223-3 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-AP0 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2001 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 51103 / Num. obs: 50501 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.031 / Χ2: 1.037 / Net I/σ(I): 37.4 |
Reflection shell | Resolution: 1.5→1.62 Å / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 7.3 / Num. measured obs: 10030 / Χ2: 0.778 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1T2C Resolution: 1.5→29.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.473 / SU ML: 0.055 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.543 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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