+Open data
-Basic information
Entry | Database: PDB / ID: 1pze | ||||||
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Title | T.gondii LDH1 apo form | ||||||
Components | lactate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NADH-dependent / tetramer / Rossmann fold | ||||||
Function / homology | Function and homology information carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 1pze.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pze.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 1pze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pze ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pze | HTTPS FTP |
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-Related structure data
Related structure data | 1pzfC 1pzgC 1pzhC 1ldgS 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: 35740.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: lactate dehydrogenase / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P90613, L-lactate dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.34 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 24% PEG 1K, 100 mM phosphate-citrate, pH 4.2, 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: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 4, 2002 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 24807 / Num. obs: 24776 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4.5 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 141594 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LDG Resolution: 1.95→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: 1.95→30 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.222 / Rfactor Rwork: 0.1876 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.016 |