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Yorodumi- PDB-1evy: CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1evy | ||||||
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Title | CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEHYDROGENASE | ||||||
Components | GLYCEROL-3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase / Rossmann fold | ||||||
Function / homology | Function and homology information glycerol-3-phosphate dehydrogenase [NAD(P)+] activity / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / glycosome / NAD binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | Suresh, S. / Turley, S. / Opperdoes, F.R. / Michels, P.A.M. / Hol, W.G.J. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: A potential target enzyme for trypanocidal drugs revealed by the crystal structure of NAD-dependent glycerol-3-phosphate dehydrogenase from Leishmania mexicana. Authors: Suresh, S. / Turley, S. / Opperdoes, F.R. / Michels, P.A. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1evy.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1evy.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 1evy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1evy ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1evy | HTTPS FTP |
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-Related 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 dimer constructed from chain A a symmetry partner generated by the two-fold. |
-Components
#1: Protein | Mass: 39317.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / Plasmid: PET3 / Production host: Escherichia coli (E. coli) References: UniProt: P90551, glycerol-3-phosphate dehydrogenase (NAD+) |
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#2: Chemical | ChemComp-MYS / |
#3: 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: 3.3 Å3/Da / Density % sol: 62.75 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: Triethanol amine pH 7.25, Sodium Citrate 0.9 M, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 125 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 46462 / Num. obs: 45712 / % possible obs: 85.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 31.65 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.317 / Num. unique all: 1691 / % possible all: 63.7 |
Reflection | *PLUS Num. measured all: 229249 |
Reflection shell | *PLUS Lowest resolution: 1.8 Å / % possible obs: 63.7 % |
-Processing
Software |
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Refinement | Resolution: 1.75→30 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: TNT
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Refinement step | Cycle: LAST / Resolution: 1.75→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.81 | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 1.8 Å / Rfactor Rfree: 0.38 / Rfactor obs: 0.36 |