+Open data
-Basic information
Entry | Database: PDB / ID: 1idf | ||||||
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Title | ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME | ||||||
Components | ISOCITRATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE (NAD(A)-CHOH(D)) | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / guanosine tetraphosphate binding / electron transport chain / tricarboxylic acid cycle / NAD binding / response to oxidative stress / magnesium ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Bolduc, J.M. / Dyer, D.H. / Scott, W.G. / Singer, P. / Sweet, R.M. / Koshland Junior, D.E. / Stoddard, B.L. | ||||||
Citation | Journal: Science / Year: 1995 Title: Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase. Authors: Bolduc, J.M. / Dyer, D.H. / Scott, W.G. / Singer, P. / Sweet, R.M. / Koshland Jr., D.E. / Stoddard, B.L. #1: Journal: Biochemistry / Year: 1991 Title: Catalytic Mechanism of Nadp+-Dependent Isocitrate Dehydrogenase: Implications from the Structures of Magnesium-Isocitrate and Nadp+ Complexes Authors: Hurley, J.H. / Dean, A.M. / Koshland Junior, D.E. / Stroud, R.M. #2: Journal: J.Biol.Chem. / Year: 1990 Title: Regulation of Isocitrate Dehydrogenase by Phosphorylation Involves No Long-Range Conformational Change in the Free Enzyme Authors: Hurley, J.H. / Dean, A.M. / Thorsness, P.E. / Koshland Junior, D.E. / Stroud, R.M. #3: Journal: Science / Year: 1990 Title: Regulation of an Enzyme by Phosphorylation at the Active Site Authors: Hurley, J.H. / Dean, A.M. / Sohl, J.L. / Koshland Junior, D.E. / Stroud, R.M. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989 Title: Structure of a Bacterial Enzyme Regulated by Phosphorylation, Isocitrate Dehydrogenase Authors: Hurley, J.H. / Thorsness, P.E. / Ramalingam, V. / Helmers, N.H. / Koshland Junior, D.E. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1idf.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1idf.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 1idf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1idf ftp://data.pdbj.org/pub/pdb/validation_reports/id/1idf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 262 |
-Components
#1: Protein | Mass: 45811.578 Da / Num. of mol.: 1 / Mutation: K230M Source method: isolated from a genetically manipulated source Details: APO ENZYME / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JLK1 / Gene: ICD / Variant: ICD(-) (DEFICIENT IN WT IDH GENE) / Plasmid: PTK513 / Gene (production host): ICD Production host: PEMBL (DENTE ET AL 1983 NUC ACIDS RES 11,1645) References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.53 Å3/Da / Density % sol: 72.84 % Description: THE MERGING R VALUE GIVEN HERE IS CRYSTAL TO CRYSTAL. THE MERGING R VALUE FOR INDIVIDUAL CRYSTALS IS 0.068, 0.072. DATA WAS COLLECTED FROM TWO SEPARATE CRYSTALS AND MERGED TOGETHER WITH PROTSYS. | ||||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 73 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.4 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 6, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 24707 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.095 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Rmerge(I) obs: 0.095 |
-Processing
Software |
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Refinement | Highest resolution: 2.5 Å / σ(F): 2
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Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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