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- PDB-1gd1: STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gd1 | |||||||||
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Title | STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.8 ANGSTROMS RESOLUTION | |||||||||
![]() | HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | |||||||||
![]() | OXIDOREDUCTASE(ALDEHYDE(D)-NAD(A)) | |||||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Skarzynski, T. / Moody, P.C.E. / Wonacott, A.J. | |||||||||
![]() | ![]() Title: Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 A resolution. Authors: Skarzynski, T. / Moody, P.C. / Wonacott, A.J. #1: ![]() 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 Escherichia Coli Authors: Branlant, C. / Oster, T. / Branlant, G. #2: ![]() Title: Coenzyme-Induced Conformational Changes in Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophillus Authors: Skarzynski, T. / Wonacott, A.J. #3: ![]() Title: Structural Evidence for Ligand-Induced Sequential Conformational Changes in Glyceraldehyde 3-Phosphate Dehydrogenase Authors: Leslie, A.G.W. / Wonacott, A.J. #4: ![]() Title: Coenzyme Binding in Crystals of Glyceraldehyde-3-Phosphate Dehydrogenase Authors: Leslie, A.G.W. / Wonacott, A.J. #5: ![]() Title: Glyceraldehyde-3-Phosphate Dehydrogenase Authors: Dalziel, K. / Mcferran, N.V. / Wonacott, A.J. #6: ![]() Title: Enzymes from Thermophilic Bacteria Authors: Walker, J.E. #7: ![]() 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: ![]() Title: Coenzyme Binding and Co-Operativity in D-Glyceraldehyde 3-Phosphate Dehydrogenase Authors: Biesecker, G. / Wonacott, A.J. #9: ![]() Title: Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus Authors: Suzuki, K. / Harris, J.I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 277.9 KB | Display | ![]() |
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PDB format | ![]() | 223.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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 CORRESPONDS TO A TWO-FOLD ROTATION ABOUT AXIS P OF THE ORTHOGONAL AXIAL SYSTEM DESCRIBED IN REMARK 5 ABOVE AND YIELDS APPROXIMATE COORDINATES FOR CHAIN *P* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 2* RECORDS BELOW (TWO-FOLD ROTATION ABOUT AXIS Q) YIELDS APPROXIMATE COORDINATES FOR CHAIN *Q* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 3* RECORDS BELOW (TWO-FOLD ROTATION ABOUT AXIS R) YIELDS APPROXIMATE COORDINATES FOR CHAIN *R* WHEN APPLIED TO CHAIN *O*. |
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Components
#1: Protein | Mass: 35991.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Cell line: 293 / Gene: BACILLUS STEAROTHERMOPHILUS / Gene (production host): BACILLUS STEAROTHERMOPHILUS / Strain (production host): 293 References: UniProt: P00362, ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-NAD / ![]() #4: 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.64 % |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 116031 / % possible obs: 81 % / Rmerge(I) obs: 0.073 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 1.8 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 3 / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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