+Open data
-Basic information
Entry | Database: PDB / ID: 1pzg | ||||||
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Title | T.gondii LDH1 complexed with APAD and sulfate at 1.6 Angstroms | ||||||
Components | lactate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / apicomplexa / APAD / tetramer / Rossmann fold | ||||||
Function / homology | Function and homology information lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kavanagh, K.L. / Elling, R.A. / Wilson, D.K. | ||||||
Citation | Journal: Biochemistry / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pzg.cif.gz | 267.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pzg.ent.gz | 216.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pzg_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1pzg_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1pzg_validation.xml.gz | 53.8 KB | Display | |
Data in CIF | 1pzg_validation.cif.gz | 74.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pzg ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pzg | HTTPS FTP |
-Related structure data
Related structure data | 1pzeC 1pzfSC 1pzhC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35816.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: LDH1 / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P90613, L-lactate dehydrogenase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-A3D / #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % | ||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2002 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 182018 / Num. obs: 167180 / % possible obs: 91.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.036 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.6 / % possible all: 92.5 |
Reflection | *PLUS Num. measured all: 451492 |
Reflection shell | *PLUS % possible obs: 92.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PZF Resolution: 1.6→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: 1.6→30 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 167149 / Rfactor Rfree: 0.1976 / Rfactor Rwork: 0.1762 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.01 |