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- PDB-1cw4: CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cw4 | ||||||
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Title | CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA-KETOGLUTARATE | ||||||
![]() | ISOCITRATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / Isocitrate Dehydrogenase / mutant | ||||||
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 | ![]() ![]() | ||||||
![]() | Stroud, M.R. / Finer-Moore, J. | ||||||
![]() | ![]() Title: Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase. Authors: Cherbavaz, D.B. / Lee, M.E. / Stroud, R.M. / Koshland Jr., D.E. #1: ![]() Title: Mutational Analysis of the Catalytic Residues Lysine 230 and Tyrosine 160 in the NADP+ Dependent Isocitrate dehydrogenase from Escherichia coli Authors: Lee, M.E. / Dyer, D.H. / Klein, O.D. / Stoddard, B.L. / Koshland Jr., D.E. #2: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.1 KB | Display | ![]() |
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PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.6 KB | Display | ![]() |
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Full document | ![]() | 450.9 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | The biological assembly is a dimer constructed from chain A by the crystallographic symmetry operation (Y,X,-Z) |
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Components
#1: Protein | Mass: 45811.578 Da / Num. of mol.: 1 / Mutation: K230M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: VARIANT OF E. COLI STRAIN JLK1 WITH NO WILD- TYPE ISOCITRATE DEHYDROGENASE GENE Plasmid: PTK513 / Production host: ![]() ![]() References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-AKG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.57 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: AMMONIUM SULFATE, DTT, NAN3, MN-ALPHA-KETOGLUTARATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. all: 41038 / Num. obs: 40761 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.6 |
Reflection | *PLUS Num. obs: 41038 / Num. measured all: 187148 |
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Processing
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Refinement | Resolution: 2.1→5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3080652.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 17.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.22 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 40761 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.19 Å / Rfactor Rwork: 0.219 |