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Yorodumi- PDB-1a7k: GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A MONOCLIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a7k | ||||||
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Title | GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A MONOCLINIC CRYSTAL FORM | ||||||
Components | GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / GLYCOSOME / TRYPANOSOME | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glycosome / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kim, H. / Hol, W.G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure. Authors: Kim, H. / Hol, W.G. #1: Journal: Biochemistry / Year: 1995 Title: Crystal Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Leishmania Mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site Authors: Kim, H. / Feil, I.K. / Verlinde, C.L. / Petra, P.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 | 1a7k.cif.gz | 276.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a7k.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a7k_validation.pdf.gz | 687.5 KB | Display | wwPDB validaton report |
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Full document | 1a7k_full_validation.pdf.gz | 726.4 KB | Display | |
Data in XML | 1a7k_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 1a7k_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a7k ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a7k | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999472, 0.030711, -0.010656), Vector: |
-Components
#1: Protein | Mass: 38953.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: ONE BOUND NAD AND TWO BOUND PHOSPHATES PER MONOMER / Source: (gene. exp.) Leishmania mexicana (eukaryote) / Cell line: BL21 / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS References: UniProt: Q27890, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NAD / |
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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: 2.32 Å3/Da / Density % sol: 46.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 Details: VAPOR DIFFUSION: 100 MM SODIUM PHOSPHATE, 27.5% PEG-1000 PH 7.0 (PH ADJUSTED WITH 100 MM CITRIC ACID), vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Oct 2, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 28710 / % possible obs: 81 % / Redundancy: 2.5 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.071 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.481 / % possible all: 81 |
Reflection | *PLUS Num. measured all: 78266 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 81 % / Rmerge(I) obs: 0.481 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TRYPANOSOMA BRUCEI GAPDH Resolution: 2.8→8 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.8 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.338 |