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Yorodumi- PDB-1sow: T. gondii bradyzoite-specific LDH (LDH2) in complex with NAD and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sow | ||||||
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Title | T. gondii bradyzoite-specific LDH (LDH2) in complex with NAD and oxalate | ||||||
Components | L-lactate dehydrogenaseLactate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / tetramer / NAD-binding | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / L-lactate dehydrogenase activity / carboxylic acid metabolic process Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kavanagh, K.L. / Wilson, D.K. | ||||||
Citation | Journal: To be Published Title: Structure of apo and ternary forms of Toxoplasma gondii LDH2 Authors: Kavanagh, K.L. / Wilson, D.K. | ||||||
History |
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Remark 999 | SEQUENCE Authors informed that the primary sequence corresponds to the sequence published in Gene ...SEQUENCE Authors informed that the primary sequence corresponds to the sequence published in Gene (1997)184:1-12. This sequence has an Asn at residue 209A and not Ser. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sow.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sow.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sow.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/1sow ftp://data.pdbj.org/pub/pdb/validation_reports/so/1sow | HTTPS FTP |
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-Related structure data
Related structure data | 1sovSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35530.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27797, L-lactate dehydrogenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.01 Å3/Da / Density % sol: 59.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 10% PEG-MME 5000, 0.6 M magnesium acetate, 100 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 67210 / Num. obs: 67007 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.97 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1sov, chain A Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.93 Å |