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Yorodumi- PDB-1nqo: Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Repl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nqo | ||||||
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Title | Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ser Complexed With Nad+ and D-Glyceraldehyde-3-Phosphate | ||||||
Components | Glyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Glycolysis / NAD | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.01 Å | ||||||
Authors | Didierjean, C. / Corbier, C. / Fatih, M. / Favier, F. / Boschi-Muller, S. / Branlant, G. / Aubry, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of two ternary complexes of phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus stearothermophilus with NAD and D-Glyceraldehyde-3-Phosphate Authors: Didierjean, C. / Corbier, C. / Fatih, M. / Favier, F. / Boschi-Muller, S. / Branlant, G. / Aubry, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nqo.cif.gz | 276.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nqo.ent.gz | 222.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nqo_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1nqo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1nqo_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 1nqo_validation.cif.gz | 78.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqo ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqo | HTTPS FTP |
-Related structure data
Related structure data | 1nptC 1nq5SC 1nqaC 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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2 |
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3 |
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Unit cell |
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Details | The second part of the first biological tetramer is generated by the symmetry operator (1-x, y, 2-z). / The second part of the second biological tetramer is generated by the symmetry operator (-x, y, 1-z). |
-Components
#1: Protein | Mass: 35974.984 Da / Num. of mol.: 4 / Mutation: C149S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: GAP / Plasmid: pBluescriptII / Production host: Escherichia coli (E. coli) References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-G3H / #4: 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: 2.09 Å3/Da / Density % sol: 40.69 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, sodium acetate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.9 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Mar 17, 1999 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→20 Å / Num. all: 78775 / Num. obs: 78775 / % possible obs: 92.8 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.01→2.07 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.2 / % possible all: 74.8 |
Reflection | *PLUS Num. obs: 77562 |
Reflection shell | *PLUS % possible obs: 74.8 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1NQ5 Resolution: 2.01→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.01→8 Å
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LS refinement shell | Resolution: 2.01→2.07 Å /
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.235 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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