+Open data
-Basic information
Entry | Database: PDB / ID: 1ihy | ||||||
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Title | GAPDH complexed with ADP-ribose | ||||||
Components | GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / GAPDH / D-glyceraldehyde-3-phosphate dehydrogenase / ADP-ribose | ||||||
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: 3 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 | 1ihy.cif.gz | 258.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ihy.ent.gz | 209.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ihy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ihy ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ihy | 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-APR / #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: 3.22 Å3/Da / Density % sol: 61.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: ammonium sulphate, pH 6.1, VAPOR DIFFUSION, HANGING 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: 3→30 Å / Num. obs: 35186 / % possible obs: 97.2 % / Redundancy: 6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / Num. unique all: 3566 / % possible all: 98.5 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 97 % / Num. measured all: 92755 |
Reflection shell | *PLUS Highest resolution: 3 Å / % possible obs: 98.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→24.37 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4824928.02 / 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: 34.12 Å2 / ksol: 0.351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→24.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.196 / Rfactor Rwork: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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