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- PDB-4ajc: 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ajc | ||||||
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Title | 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, calcium(II) and adenine nucleotide phosphate | ||||||
![]() | NADP ISOCITRATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / OXIDATIVE BETA-DECARBOXYLATION | ||||||
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 | ![]() ![]() | ||||||
![]() | Goncalves, S. / Miller, S.P. / Carrondo, M.A. / Dean, A.M. / Matias, P.M. | ||||||
![]() | ![]() Title: Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase. Authors: Goncalves, S. / Miller, S.P. / Carrondo, M.A. / Dean, A.M. / Matias, P.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.4 KB | Display | ![]() |
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PDB format | ![]() | 79.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.6 KB | Display | ![]() |
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Full document | ![]() | 806.7 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aj3C ![]() 4ajaC ![]() 4ajbC ![]() 4ajrC ![]() 4ajsC ![]() 1ai2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45811.578 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q1RD16, UniProt: P08200*PLUS, isocitrate dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 433 molecules ![](data/chem/img/A2P.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-A2P / |
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#3: Chemical | ChemComp-AKG / |
#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72 % / Description: NONE |
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Crystal grow | Details: 1.85M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER AXS PT135 / Detector: CCD / Details: MONTEL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.4 Å / Num. obs: 36981 / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AI2 Resolution: 2.3→44.302 Å / SU ML: 0.64 / σ(F): 0 / Phase error: 20.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.616 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→44.302 Å
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Refine LS restraints |
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LS refinement shell |
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