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Yorodumi- PDB-1n1e: Crystal structure of Leishmania mexicana Glycerol-3-phosphate deh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n1e | ||||||
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Title | Crystal structure of Leishmania mexicana Glycerol-3-phosphate dehydrogenase complexed with DHAP and NAD | ||||||
Components | glycerol-3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / NAD BINDING DOMAIN | ||||||
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 / glycerophospholipid biosynthetic process / NADH oxidation / glycosome / NAD binding / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Choe, J. / Hol, W.G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Leishmania mexicana Glycerol-3-phosphate Dehydrogenase Showed Conformational Changes Upon Binding a Bi-substrate Adduct Authors: Choe, J. / Guerra, D. / Michels, P.A.M. / Hol, W.G.J. | ||||||
History |
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Remark 600 | HETEROGEN THE LIGAND IS AN ADDUCT FORMED FROM DHAP (DIHYDROXYACETONE PHOSPHATE) COVALENTLY BOUND TO NAD. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n1e.cif.gz | 147.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n1e.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 1n1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/1n1e ftp://data.pdbj.org/pub/pdb/validation_reports/n1/1n1e | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39317.828 Da / Num. of mol.: 2 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+) #2: Chemical | #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: 2.96 Å3/Da / Density % sol: 58.41 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 8000, ammonium sulfate, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 62860 / Num. obs: 62860 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7102 / Rsym value: 0.306 / % possible all: 61.5 |
Reflection | *PLUS Num. obs: 66338 / % possible obs: 92.3 % / Num. measured all: 793825 |
Reflection shell | *PLUS % possible obs: 61.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.829 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.116 / 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: 21.128 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.896→1.945 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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