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Open data
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Basic information
Entry | Database: PDB / ID: 1pzf | ||||||
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Title | T.gondii LDH1 ternary complex with APAD+ and oxalate | ||||||
![]() | lactate dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / APAD / Rossmann fold / tetramer / apicomplexa | ||||||
Function / homology | ![]() lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kavanagh, K.L. / Elling, R.A. / Wilson, D.K. | ||||||
![]() | ![]() Title: Structure of Toxoplasma gondii LDH1: Active-Site Differences from Human Lactate Dehydrogenases and the Structural Basis for Efficient APAD+ Use. Authors: Kavanagh, K.L. / Elling, R.A. / Wilson, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.4 KB | Display | ![]() |
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PDB format | ![]() | 212.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 52.4 KB | Display | |
Data in CIF | ![]() | 71.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pzeC ![]() 1pzgC ![]() 1pzhSC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 35740.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-OXL / #3: Chemical | ChemComp-A3D / #4: 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: 50.34 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.9 M ammonium sulfate, 100 mM acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
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 QUANTUM 4 / Detector: CCD / Date: Mar 15, 2002 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 70916 / Num. obs: 70313 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.121 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.386 / % possible all: 91.7 |
Reflection | *PLUS Num. measured all: 224085 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 91.7 % / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1PZH Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Xplor file |
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Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.41 |