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Yorodumi- PDB-1dc3: STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dc3 | ||||||
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Title | STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES | ||||||
Components | GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / GAPDH / SUBSTRATE | ||||||
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 / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Yun, M. / Park, C.G. / Kim, J.Y. / Park, H.W. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes. Authors: Yun, M. / Park, C.G. / Kim, J.Y. / Park, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dc3.cif.gz | 134.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dc3.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dc3_validation.pdf.gz | 424.8 KB | Display | wwPDB validaton report |
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Full document | 1dc3_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 1dc3_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 1dc3_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/1dc3 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/1dc3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35446.238 Da / Num. of mol.: 2 / Fragment: APO / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) References: UniProt: P0A9B2, 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: 4 Å3/Da / Density % sol: 69.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, MAGNESIUM CHLORIDE, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9792 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 38265 / Num. obs: 38265 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 27.6 % / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.36 % / Rmerge(I) obs: 0.216 / % possible all: 100 |
Reflection | *PLUS % possible obs: 99.8 % / Num. measured all: 1055831 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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