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Yorodumi- PDB-2gd1: COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gd1 | ||||||
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Title | COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILLUS | ||||||
Components | APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE(ALDEHYDE(D)-NAD(A)) | ||||||
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 / Resolution: 2.5 Å | ||||||
Authors | Skarzynski, T. / Wonacott, A.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1988 Title: Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus. Authors: Skarzynski, T. / Wonacott, A.J. #1: Journal: Gene / Year: 1989 Title: Nucleotide Sequence Determination of the DNA Region Coding for Bacillus Stearothermophilus Glyceraldehyde-3-Phosphate Dehydrogenase and of the Flanking DNA Regions Required for its Expression in Escherichia Coli Authors: Branlant, C. / Oster, T. / Branlant, G. #2: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus at 1.8 Angstroms Resolution Authors: Skarzynski, T. / Moody, P.C.E. / Wonacott, A.J. #3: Journal: J.Mol.Biol. / Year: 1984 Title: Structural Evidence for Ligand-Induced Sequential Conformational Changes in Glyceraldehyde 3-Phosphate Dehydrogenase Authors: Leslie, A.G.W. / Wonacott, A.J. #4: Journal: J.Mol.Biol. / Year: 1983 Title: Coenzyme Binding in Crystals of Glyceraldehyde-3-Phosphate Dehydrogenase Authors: Leslie, A.G.W. / Wonacott, A.J. #5: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981 Title: Glyceraldehyde-3-Phosphate Dehydrogenase Authors: Dalziel, K. / Mcferran, N.V. / Wonacott, A.J. #6: Journal: Proc.FEBS Meet. / Year: 1978 Title: Enzymes from Thermophilic Bacteria Authors: Walker, J.E. #7: Journal: Nature / Year: 1977 Title: Sequence and Structure of D-Glyceraldehyde 3-Phosphate Dehydrogenase from Bacillus Stearothermophilus Authors: Biesecker, G. / Harris, J.I. / Thierry, J.C. / Walker, J.E. / Wonacott, A.J. #8: Journal: Biochem.Soc.Trans. / Year: 1977 Title: Coenzyme Binding and Co-Operativity in D-Glyceraldehyde 3-Phosphate Dehydrogenase Authors: Biesecker, G. / Wonacott, A.J. #9: Journal: FEBS Lett. / Year: 1971 Title: Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus Authors: Suzuki, K. / Harris, J.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gd1.cif.gz | 266.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gd1.ent.gz | 214.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/2gd1 ftp://data.pdbj.org/pub/pdb/validation_reports/gd/2gd1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATION PROVIDED ON THE *MTRIX 1* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *P* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 2* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *Q* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 3* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *R* WHEN APPLIED TO CHAIN *O*. |
-Components
#1: Protein | Mass: 35991.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Cell line: 293 References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | THE NUMBERING SCHEME USED IN THIS ENTRY MAXIMIZES THE HOMOLOGY BETWEEN SEQUENCES OF GAPDH FROM ...THE NUMBERING SCHEME USED IN THIS ENTRY MAXIMIZES THE HOMOLOGY BETWEEN SEQUENCES OF GAPDH FROM VARIOUS SOURCES. THE AMINO ACID SEQUENCE USED IS BASED ON THE GENE SEQUENCE (SEE REFERENCE 1 ABOVE) AND CONTAINS 20 DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.76 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.6 / Method: microdialysis / Details: referred to FEBS Lett.13.217-220 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 55743 / % possible obs: 95.4 % / Rmerge(I) obs: 0.098 / Num. measured all: 183964 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 2.5 Å /
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Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 7 Å / Rfactor obs: 0.177 / Highest resolution: 2.5 Å / Num. reflection all: 53315 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |