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- PDB-3b1k: Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b1k | ||||||
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Title | Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the absence of copper from Synechococcus elongatus | ||||||
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![]() | OXIDOREDUCTASE/PROTEIN BINDING / alpha/beta fold / OXIDOREDUCTASE-PROTEIN BINDING complex | ||||||
Function / homology | ![]() negative regulation of reductive pentose-phosphate cycle / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matsumura, H. / Kai, A. / Inoue, T. | ||||||
![]() | ![]() Title: Structure Basis for the Regulation of Glyceraldehyde-3-Phosphate Dehydrogenase Activity via the Intrinsically Disordered Protein CP12. Authors: Matsumura, H. / Kai, A. / Maeda, T. / Tamoi, M. / Satoh, A. / Tamura, H. / Hirose, M. / Ogawa, T. / Kizu, N. / Wadano, A. / Inoue, T. / Shigeoka, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 284 KB | Display | ![]() |
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PDB format | ![]() | 229.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 76.7 KB | Display | |
Data in CIF | ![]() | 100.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b1jC ![]() 3b20C ![]() 3d2iS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37032.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9R6W2, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #2: Protein/peptide | Mass: 2830.917 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 51-75 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20%(v/v) PEG3350, 0.2M magnesium acetate., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Nov 16, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 22942 / Num. obs: 22942 / % possible obs: 89 % / Observed criterion σ(I): 5.1 / Rmerge(I) obs: 0.147 |
Reflection shell | Resolution: 3.3→3.36 Å / Rmerge(I) obs: 0.35 / % possible all: 85.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3D2I Resolution: 3.302→26.062 Å / SU ML: 0.61 / σ(F): 0 / Phase error: 38.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.756 Å2 / ksol: 0.273 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.302→26.062 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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