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Yorodumi- PDB-1crw: CRYSTAL STRUCTURE OF APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1crw | ||||||
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Title | CRYSTAL STRUCTURE OF APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR AT 2.0A RESOLUTION | ||||||
Components | D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / FREE-NAD GAPDH | ||||||
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 / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Shen, Y. / Li, J. / Song, S. / Lin, Z. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2000 Title: Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor. Authors: Shen, Y.Q. / Li, J. / Song, S.Y. / Lin, Z.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Structure of Holo-Glyceraldehyde-3-phosphate Dehydrogenase from Palinurus Versicolor Refined at 2A Resolution Authors: Song, S. / Li, J. / Lin, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1crw.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1crw.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 1crw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/1crw ftp://data.pdbj.org/pub/pdb/validation_reports/cr/1crw | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological tetramer is obtained by the two-fold symmetry operation of chain G and chain R. |
-Components
#1: Protein | Mass: 35767.004 Da / Num. of mol.: 2 / 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: 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: 3.28 Å3/Da / Density % sol: 62.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 18K |
Crystal grow | *PLUS Details: Song, S.Y., (1988) Sci. Chin., 3, 313. |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
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Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 10, 1990 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 154634 / Num. obs: 54995 / Observed criterion σ(F): 0 / Redundancy: 1.4 % / Rmerge(I) obs: 0.0706 |
Reflection shell | Highest resolution: 1.8 Å / Num. unique all: 54995 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. obs: 45695 / % possible obs: 74.5 % / Num. measured all: 136230 |
-Processing
Software |
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Refinement | Resolution: 2→6 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.179 / Rfactor Rfree: 0.228 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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