[English] 日本語
![](img/lk-miru.gif)
- PDB-1ai3: ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTU... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ai3 | ||||||
---|---|---|---|---|---|---|---|
Title | ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES | ||||||
![]() | ISOCITRATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / NADP / PHOSPHORYLATION / GLYOXYLATE BYPASS | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stoddard, B.L. / Mesecar, A. / Koshland Junior, D.E. | ||||||
![]() | ![]() Title: Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences. Authors: Mesecar, A.D. / Stoddard, B.L. / Koshland Jr., D.E. #1: ![]() Title: Determinants of Cofactor Specificity in Isocitrate Dehydrogenase: Structure of an Engineered Nadp+--> Nad+ Specificity-Reversal Mutant Authors: Hurley, J.H. / Chen, R. / Dean, A.M. #2: ![]() Title: Structure of Isocitrate Dehydrogenase with Isocitrate, Nicotinamide Adenine Dinucleotide Phosphate, and Calcium at 2.5-A Resolution: A Pseudo-Michaelis Ternary Complex Authors: Stoddard, B.L. / Dean, A. / Koshland Junior, D.E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 78.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 522.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ai2C ![]() 1isoS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45809.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
---|---|
#2: Chemical | ChemComp-NDO / |
#3: Chemical | ChemComp-ICT / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.31 Å3/Da / Density % sol: 71.46 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.4 / Method: unknownDetails: Hurley, J.H., (1989) Proc. Natl. Acad. Sci. U.S.A., 86, 8635. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1996 / Details: TORROIDAL MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 62143 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.18 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 198342 / Rmerge(I) obs: 0.06 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ISO Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|