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Yorodumi- PDB-3b1j: Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b1j | ||||||
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Title | Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the presence of copper from Synechococcus elongatus | ||||||
Components |
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Keywords | OXIDOREDUCTASE/PROTEIN BINDING / alpha/beta fold / OXIDOREDUCTASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information 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 | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Matsumura, H. / Kai, A. / Inoue, T. | ||||||
Citation | Journal: Structure / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b1j.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b1j.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 3b1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b1j_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3b1j_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3b1j_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 3b1j_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/3b1j ftp://data.pdbj.org/pub/pdb/validation_reports/b1/3b1j | HTTPS FTP |
-Related structure data
Related structure data | 3b1kC 3b20C 3d2iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37032.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: gap2, Synpcc7942_1742 / Production host: Escherichia coli (E. coli) References: UniProt: Q9R6W2, glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) #2: Protein/peptide | Mass: 2830.917 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 51-75 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: cp12, Synpcc7942_0361 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6BBK3 #3: Chemical | #4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 52.78 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Date: Dec 7, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 42240 / Num. obs: 42240 / % possible obs: 99.8 % / Observed criterion σ(I): 0.187 / Rmerge(I) obs: 0.105 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.435 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D2I Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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