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- PDB-2dbv: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dbv | ||||||
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Title | GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLACED BY GLY, LEU 187 REPLACED BY ALA, AND PRO 188 REPLACED BY SER COMPLEXED WITH NADP+ | ||||||
![]() | GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / NAD(P) SELECTIVITY | ||||||
Function / homology | ![]() glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Didierjean, C. / Rahuel-Clermont, S. / Vitoux, B. / Dideberg, O. / Branlant, G. / Aubry, A. | ||||||
![]() | ![]() Title: A crystallographic comparison between mutated glyceraldehyde-3-phosphate dehydrogenases from Bacillus stearothermophilus complexed with either NAD+ or NADP+. Authors: Didierjean, C. / Rahuel-Clermont, S. / Vitoux, B. / Dideberg, O. / Branlant, G. / Aubry, A. #1: ![]() Title: Nucleotide Sequence Determination of the DNA Region Coding for Bacillus Stearothermophilus Glyceraldehyde-3-Phosphate Dehydrogenase and of the Flanking DNA Regions Required for its Expression in Escherichia Coli Authors: Branlant, C. / Oster, T. / Branlant, G. #2: ![]() Title: Structure of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus at 1.8 A Resolution Authors: Skarzynski, T. / Moody, P.C. / Wonacott, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.7 KB | Display | ![]() |
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PDB format | ![]() | 217.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 55.5 KB | Display | |
Data in CIF | ![]() | 75.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 35880.895 Da / Num. of mol.: 4 / Mutation: D32G, L187A, P188S Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH NADP+ Source: (gene. exp.) ![]() ![]() Cellular location: CYTOPLASM / Gene: GAP / Gene (production host): BACILLUS STEAROTHERMOPHILUS / Production host: ![]() ![]() References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NDP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.76 % Description: MUTANT CRYSTALS ARE ISOMORPHOUS TO THAT OF THE WILD-TYPE HOLOENZYME (1GD1) CRYSTALS | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.9 / Details: pH 6.9 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 70186 / % possible obs: 84.1 % / Rsym value: 0.097 |
Reflection | *PLUS Redundancy: 2.4 % / Num. measured all: 65530 / Rmerge(I) obs: 0.097 |
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Processing
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Refinement | Resolution: 2.2→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 27.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.31 |