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Yorodumi- PDB-1grp: REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1grp | ||||||
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Title | REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115 | ||||||
Components | ISOCITRATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE (NAD(A)-CHOH(D)) / OXIDOREDUCTASE / NADP / PHOSPHORYLATION / GLYOXYLATE BYPASS | ||||||
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 | Grobler, J.A. / Hurley, J.H. | ||||||
Citation | Journal: Protein Sci. / Year: 1996 Title: Second-site suppression of regulatory phosphorylation in Escherichia coli isocitrate dehydrogenase. Authors: Chen, R. / Grobler, J.A. / Hurley, J.H. / Dean, A.M. #1: 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. #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. / Koshland Junior, D.E. / Stroud, R.M. #3: 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 | 1grp.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1grp.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 1grp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1grp_validation.pdf.gz | 386.8 KB | Display | wwPDB validaton report |
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Full document | 1grp_full_validation.pdf.gz | 395.4 KB | Display | |
Data in XML | 1grp_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1grp_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/1grp ftp://data.pdbj.org/pub/pdb/validation_reports/gr/1grp | HTTPS FTP |
-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: 45794.594 Da / Num. of mol.: 1 / Mutation: N115L 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-MG / |
#3: Chemical | ChemComp-ICT / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.54 Å3/Da / Density % sol: 72.9 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.4 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.54 |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 28004 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.118 |
Reflection | *PLUS Rmerge(I) obs: 0.118 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 66.1 % / Num. unique obs: 1957 / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.9 |
-Processing
Software |
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Refinement | Resolution: 2.5→6 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |