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Yorodumi- PDB-1ihx: Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ihx | ||||||
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Title | Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry | ||||||
Components | GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / GAPDH / asymmetry / SNAD | ||||||
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 | Palinurus versicolor (painted spiny lobster) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Shen, Y.-Q. / Song, S.-Y. / Lin, Z.-J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues. Authors: Shen, Y.Q. / Song, S.Y. / Lin, Z.J. #1: Journal: J.Struct.Biol. / Year: 2000 Title: Structure of apo-D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor Authors: Shen, Y.-Q. / Li, J. / Song, S.-Y. / Lin, Z.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ihx.cif.gz | 261.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ihx.ent.gz | 213.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ihx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ihx ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ihx | HTTPS FTP |
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-Related 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: 35855.109 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Palinurus versicolor (painted spiny lobster) Tissue: TAIL MUSCLE References: UniProt: P56649, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SND / #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: 3.23 Å3/Da / Density % sol: 61.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: ammonium sulphate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal grow | *PLUS Details: Shen, Y.O., (2000) Chin. Sci. Bull., 45, 1199. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SEALED TUBE / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 44055 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 49.6 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / Num. unique all: 4379 / % possible all: 97.9 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 98 % / Num. measured all: 119278 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 97.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4510081.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.77 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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