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Yorodumi- PDB-1nqa: Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Repl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nqa | ||||||
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Title | Glyceraldehyde-3-Phosphate Dehydrogenase Mutant With Cys 149 Replaced By Ala 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: 2.2 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 | 1nqa.cif.gz | 277.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nqa.ent.gz | 223.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqa ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqa | HTTPS FTP |
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-Related structure data
Related structure data | 1nptSC 1nq5C 1nqoC S: Starting model for refinement C: citing same article (ref.) |
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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: 35958.984 Da / Num. of mol.: 4 / Mutation: C149A 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: 2.79 Å3/Da / Density % sol: 55.61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, sodium acetate, pH 4.6, 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: May 21, 1998 / 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: 2.2→15 Å / Num. all: 86696 / Num. obs: 86696 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.7 / % possible all: 98.9 |
Reflection | *PLUS Num. obs: 83284 |
Reflection shell | *PLUS % possible obs: 98.9 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1NPT Resolution: 2.2→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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LS refinement shell | Resolution: 2.2→2.28 Å
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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