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Yorodumi- PDB-1i32: LEISHMANIA MEXICANA GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i32 | ||||||
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Title | LEISHMANIA MEXICANA GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN COMPLEX WITH INHIBITORS | ||||||
Components | GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / enzyme / dehydrogenase | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycosome / glycolytic process / glucose metabolic process / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Suresh, S. / Bressi, J.C. / Kennedy, K.J. / Verlinde, C.L.M.J. / Gelb, M.H. / Hol, W.G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Conformational changes in Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase induced by designed inhibitors. Authors: Suresh, S. / Bressi, J.C. / Kennedy, K.J. / Verlinde, C.L. / Gelb, M.H. / 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 | 1i32.cif.gz | 424.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i32.ent.gz | 348.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/1i32 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/1i32 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38953.504 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: Q27890, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NMD / #3: 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: 2.4 Å3/Da / Density % sol: 48.83 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: PEG1000, 100mM TEA, 250mM NaCl, 5mM DTT, 1mM PMSF 15mM HEPES, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2000 |
Radiation | Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→15 Å / Num. all: 65878 / Num. obs: 65878 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.18 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.6→2.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.289 / % possible all: 71.7 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 407373 |
Reflection shell | *PLUS % possible obs: 71.7 % / Mean I/σ(I) obs: 4.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.368 / Rfactor obs: 0.299 |