[English] 日本語
Yorodumi- PDB-1dbv: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE MUTANT WITH ASP 32 REPLA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dbv | ||||||
---|---|---|---|---|---|---|---|
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 NAD+ | ||||||
Components | GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / NAD(P) SELECTIVITY | ||||||
Function / homology | Function and homology information 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 | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Didierjean, C. / Rahuel-Clermont, S. / Vitoux, B. / Dideberg, O. / Branlant, G. / Aubry, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 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: Journal: Gene / Year: 1989 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: Journal: J.Mol.Biol. / Year: 1987 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dbv.cif.gz | 265.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dbv.ent.gz | 216.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dbv_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dbv_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1dbv_validation.xml.gz | 52.4 KB | Display | |
Data in CIF | 1dbv_validation.cif.gz | 72.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/1dbv ftp://data.pdbj.org/pub/pdb/validation_reports/db/1dbv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-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 NAD+ Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Cellular location: CYTOPLASM / Gene: GAP / Gene (production host): BACILLUS STEAROTHERMOPHILUS / Production host: Escherichia coli (E. coli) / Strain (production host): DF221 References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.51 % Description: THE MUTANT CRYSTALS ARE ISOMORPHOUS TO THE CRYSTALS OF THE WILD-TYPE HOLOENZYME (PDB ENTRY 1GD1). | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.9 / Details: pH 6.9 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 297 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Apr 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. obs: 45468 / % possible obs: 85 % / Observed criterion σ(I): 0 / Rsym value: 0.07 |
Reflection | *PLUS % possible obs: 81 % / Rmerge(I) obs: 0.068 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|