+Open data
-Basic information
Entry | Database: PDB / ID: 1b7g | ||||||
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Title | GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE | ||||||
Components | PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE / ARCHAEA / HYPERTHERMOPHILE / GAPDH / HYPERTHERMOPHILIC DEHYDROGENASE | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) / 4-hydroxy-tetrahydrodipicolinate reductase / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / lysine biosynthetic process via diaminopimelate / glycolytic process / NAD binding / NADP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.05 Å | ||||||
Authors | Isupov, M.N. / Littlechild, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of the glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus. Authors: Isupov, M.N. / Fleming, T.M. / Dalby, A.R. / Crowhurst, G.S. / Bourne, P.C. / Littlechild, J.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Characterization, Crystallization and Preliminary X-Ray Investigation of Glyceraldehyde-3-Phosphate Dehydrogenase from the Hyperthermophilic Archaeon Sulfolobus Solfataricus Authors: Fleming, T.M. / Jones, C.E. / Piper, P.W. / Cowan, D.A. / Isupov, M.N. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b7g.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b7g.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 1b7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b7g ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b7g | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.62399, 0.38067, 0.68244), Vector: |
-Components
#1: Protein | Mass: 37631.617 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) References: UniProt: P39460, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | VAL O 2, FOR EASE OF CLONING OF THE GENE IN E.COLI VAL Q 2, FOR EASE OF CLONING OF THE GENE IN E. ...VAL O 2, FOR EASE OF CLONING OF THE GENE IN E.COLI VAL Q 2, FOR EASE OF CLONING OF THE GENE IN E.COLI ILE O 48, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ILE Q 48, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ALA O 51, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ALA Q 51, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES GLU O 72, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES GLU Q 72, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ASP O 73, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES ASP Q 73, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES LYS O 159, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES LYS Q 159, CONFLICT BETWEEN THE TWO PUBLISHED SEQUENCES | |
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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: 3.1 Å3/Da / Density % sol: 60 % Description: THE STRUCTURE WAS SOLVED TO 3. ANGSTROM USING IN- HOUSE DATA | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→22 Å / Num. obs: 59606 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5 |
Reflection | *PLUS Highest resolution: 2.05 Å / Lowest resolution: 22 Å / Redundancy: 5.9 % / Biso Wilson estimate: 33 Å2 |
Reflection shell | *PLUS % possible obs: 98.5 % / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.05→22 Å / SU B: 5.4 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.19
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Displacement parameters | Biso mean: 38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→22 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |