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Yorodumi- PDB-1t25: Plasmodium falciparum lactate dehydrogenase complexed with NADH a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t25 | ||||||
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Title | Plasmodium falciparum lactate dehydrogenase complexed with NADH and 3-hydroxyisoxazole-4-carboxylic acid | ||||||
Components | L-lactate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / protein-ligand complex | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. ...Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / Risco, F. / Garcia-Ochoa, S. / Gamo, F.J. / Sanz, L. / Leon, L. / Ruiz, J.R. / Gabarro, R. / Mallo, A. / De Las Heras, F.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Identification and Activity of a Series of Azole-based Compounds with Lactate Dehydrogenase-directed Anti-malarial Activity. Authors: Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / ...Authors: Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / Risco, F. / Garcia-Ochoa, S. / Gamo, F.J. / Sanz, L. / Leon, L. / Ruiz, J.R. / Gabarro, R. / Mallo, A. / De Las Heras, F.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t25.cif.gz | 81.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t25.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/1t25 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/1t25 | HTTPS FTP |
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-Related structure data
Related structure data | 1t24C 1t26C 1t2cC 1t2dC 1t2eC 1t2fC 1ldgS 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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Details | The biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: |
-Components
#1: Protein | Mass: 34977.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: LDH / Plasmid: pKK223 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q27743, L-lactate dehydrogenase |
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#2: Chemical | ChemComp-NAI / |
#3: Chemical | ChemComp-GAG / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.3 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.75 Å / Num. all: 26093 / Num. obs: 24119 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.066 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.9→1.99 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.227 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LDG Resolution: 1.9→29.75 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.482 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 12.609 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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