[English] 日本語
Yorodumi- PDB-4icd: REGULATION OF ISOCITRATE DEHYDROGENASE BY PHOSPHORYLATION INVOLVE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4icd | ||||||
---|---|---|---|---|---|---|---|
Title | REGULATION OF ISOCITRATE DEHYDROGENASE BY PHOSPHORYLATION INVOLVES NO LONG-RANGE CONFORMATIONAL CHANGE IN THE FREE ENZYME | ||||||
Components | PHOSPHORYLATED 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 / tricarboxylic acid cycle / electron transport chain / NAD binding / response to oxidative stress / magnesium ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Hurley, J.H. / Dean, A.M. / Thorsness, P.E. / Koshlandjunior, D.E. / Stroud, R.M. | ||||||
Citation | 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 Jr., D.E. / Stroud, R.M. #1: 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. #2: 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4icd.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4icd.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 4icd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4icd_validation.pdf.gz | 368.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4icd_full_validation.pdf.gz | 380.2 KB | Display | |
Data in XML | 4icd_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 4icd_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/4icd ftp://data.pdbj.org/pub/pdb/validation_reports/ic/4icd | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUE SER 113 IS A PHOSPHORYLATED SERINE. / 2: PRO 262 IS A CIS PROLINE. |
-Components
#1: Protein | Mass: 45889.543 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+) |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.8 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 5.4 / Method: unknown / Details: took J. H. Hurley et al.,from original paper | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 21162 / Observed criterion σ(F): 1 / Num. measured all: 156365 / Rmerge F obs: 0.121 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor Rwork: 0.169 / Highest resolution: 2.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
| ||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Rfactor obs: 0.169 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |