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Yorodumi- PDB-1jdj: CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jdj | ||||||
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Title | CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEHYDROGENASE IN COMPLEX WITH 2-FLUORO-6-CHLOROPURINE | ||||||
Components | GLYCEROL-3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Suresh, S. / Wisedchaisri, G. / Kennedy, K.J. / Verlinde, C.L.M.J. / Gelb, M.H. / Hol, W.G.J. | ||||||
Citation | Journal: Chem.Biol. / Year: 2002 Title: Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase. Authors: Choe, J. / Suresh, S. / Wisedchaisri, G. / Kennedy, K.J. / 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 | 1jdj.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jdj.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jdj ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jdj | HTTPS FTP |
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-Related structure data
Related structure data | 1m66C 1m67C 1n1gC 1evyS 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 | biological dimer generated by crystallographic 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: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P90551, glycerol-3-phosphate dehydrogenase (NAD+) |
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#2: Chemical | ChemComp-CFP / |
#3: Chemical | ChemComp-MYS / |
#4: 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: 3.31 Å3/Da / Density % sol: 62.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.9 M sodium citrate, 50 mM TEA pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal grow | *PLUS |
Components of the solutions | *PLUS Conc.: 0.8-0.9 M / Common name: sodium citrate |
-Data collection
Diffraction | Mean temperature: 125 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 27686 / Num. obs: 27686 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.08 % / Biso Wilson estimate: 28.44 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 7.6 / Num. unique all: 2492 / Rsym value: 0.184 / % possible all: 91.6 |
Reflection | *PLUS Redundancy: 7.1 % / Num. measured all: 196124 |
Reflection shell | *PLUS % possible obs: 91.6 % / Rmerge(I) obs: 0.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EVY Resolution: 2.2→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS / Details: CNS
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Displacement parameters | Biso mean: 31.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.2 Å / Rfactor obs: 0.215 |