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Yorodumi- PDB-9icd: CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE DEHYDROGENASE: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9icd | ||||||
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Title | CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE DEHYDROGENASE: IMPLICATIONS FROM THE STRUCTURES OF MAGNESIUM-ISOCITRATE AND NADP+ COMPLEXES | ||||||
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 | Hurley, J.H. / Dean, A.M. / Koshland Jr., D.E. / Stroud, R.M. | ||||||
Citation | 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 Jr., D.E. / Stroud, R.M. #1: 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. / Koshlandjunior, 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. / Koshlandjunior, 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. / Koshlandjunior, 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. / Koshlandjunior, 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 | 9icd.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9icd.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 9icd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/9icd ftp://data.pdbj.org/pub/pdb/validation_reports/ic/9icd | 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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Atom site foot note | 1: RESIDUE PRO 262 IS A CIS PROLINE. NOTE THAT IT IS IN A / 2: THE REGIONS 17 - 20 AND 258 - 262 ARE POORLY DEFINED. |
-Components
#1: Protein | Mass: 45809.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE PORTION OF NADP+ CORRESPONDING TO NICOTINAMIDE MONONUCLEOTIDE COULD NOT BE LOCATED IN ...THE PORTION OF NADP+ CORRESPOND |
-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 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.4 / Method: unknownDetails: taken from Hurley, J.H. et al (1989). Proc. Natl. Acad. Sci. USA, 86, 8635-8639. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 29217 / % possible obs: 96.5 % / Rmerge(I) obs: 0.115 / Num. measured all: 141100 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor Rwork: 0.181 / Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 22342 / Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d |