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Open data
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Basic information
Entry | Database: PDB / ID: 1oc4 | ||||||
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Title | Lactate dehydrogenase from Plasmodium berghei | ||||||
![]() | L-LACTATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / LACTATE DEHYDROGENASE / GLYCOLYSIS / INTERCONVERSION OF PYRUVATE AND LACTATE / 3-LAYER (ABA) SANDWICH | ||||||
Function / homology | ![]() pyruvate biosynthetic process / L-lactate dehydrogenase / carboxylic acid metabolic process / L-lactate dehydrogenase activity / glycolytic process / NAD binding / carbohydrate metabolic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Winter, V.J. / Brady, R.L. | ||||||
![]() | ![]() Title: Crystal Structure of Plasmodium Berghei Lactate Dehydrogenase Indicates the Unique Structural Differences of These Enzymes are Shared Across the Plasmodium Genus Authors: Winter, V.J. / Cameron, A. / Tranter, R. / Sessions, R.B. / 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 | ![]() | 141 KB | Display | ![]() |
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PDB format | ![]() | 109 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ldgS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.511, -0.859, -0.003), Vector: |
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Components
#1: Protein | Mass: 35295.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NICOTINAMIDE-ADENINE-DINUCLEOTIDE COFACTOR, OXAMIC ACID INHIBITOR Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q4Z783, UniProt: Q7SI97*PLUS, L-lactate dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 43.3 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 32% PEG 1500, pH 7.50 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 31653 / % possible obs: 98.8 % / Redundancy: 5.49 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.11 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.01 / % possible all: 98 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Redundancy: 5.49 % / Num. measured all: 173810 / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / Rmerge(I) obs: 0.281 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LDG Resolution: 2.3→29.49 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.163 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 33.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.49 Å
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Refine LS restraints |
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