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Yorodumi- PDB-1uxq: Structural basis for allosteric regulation and substrate specific... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uxq | ||||||
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Title | Structural basis for allosteric regulation and substrate specificity of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from Thermoproteus tenax | ||||||
Components | GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+)Glyceraldehyde-3-phosphate dehydrogenase (NADP+) | ||||||
Keywords | OXIDOREDUCTASE / GAPN / ALDH / GLUCOSE 1-PHOSPHATE / GLYCOLYSIS / REGULATION / CATALYSIS | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / metabolic process / NAD binding / NADP binding Similarity search - Function | ||||||
Biological species | THERMOPROTEUS TENAX (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lorentzen, E. / Hensel, R. / Pohl, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural Basis of Allosteric Regulation and Substrate Specificity of the Non-Phosphorylating Glyceraldehyde 3-Phosphate Dehydrogenase from Thermoproteus Tenax Authors: Lorentzen, E. / Hensel, R. / Knura, T. / Ahmed, H. / Pohl, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uxq.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uxq.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 1uxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1uxq ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1uxq | HTTPS FTP |
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-Related structure data
Related structure data | 1uxnC 1uxpC 1uxrC 1uxtC 1uxuC 1uxvC 1ky8S S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 54218.367 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: GLUCOSE 1-PHOSPHATE AND NADP(H) BOUND NONCOVALENTLY Source: (gene. exp.) THERMOPROTEUS TENAX (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O57693, glyceraldehyde-3-phosphate dehydrogenase (NADP+) | ||
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#2: Chemical | ChemComp-NAP / | ||
#3: Sugar | ChemComp-G1P / | ||
#4: Chemical | ChemComp-NA / | ||
#5: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | SER 402 LEU IS DUE TO A SEQUENCING ERROR. THE AUTHORS INDICATE THAT THE SERINE REPORTED IN SWISS- ...SER 402 LEU IS DUE TO A SEQUENCING | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6 Å3/Da / Density % sol: 80 % |
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Crystal grow | pH: 5.6 Details: 2M SODIUM FORMATE PH 5.6, 0.1 M SODIUM ACETATE PH 5.6, 1 MM GLUCOSE 1-PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8453 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8453 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 53432 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 35 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 14 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 14 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KY8 Resolution: 2.4→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 1-2 NOT MODELED, RESIDUES 499-501 AS ALANINES
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Displacement parameters | Biso mean: 57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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