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Yorodumi- PDB-4ajr: 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ajr | ||||||
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Title | 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, magnesium(II) and NADPH - The product complex | ||||||
Components | ISOCITRATE DEHYDROGENASE [NADP] | ||||||
Keywords | OXIDOREDUCTASE / OXIDATIVE BETA-DECARBOXYLATION | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / guanosine tetraphosphate binding / electron transport chain / tricarboxylic acid cycle / NAD binding / response to oxidative stress / magnesium ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.687 Å | ||||||
Authors | Goncalves, S. / Miller, S.P. / Carrondo, M.A. / Dean, A.M. / Matias, P.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ajr.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ajr.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ajr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/4ajr ftp://data.pdbj.org/pub/pdb/validation_reports/aj/4ajr | HTTPS FTP |
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-Related structure data
Related structure data | 4aj3C 4ajaC 4ajbC 4ajcC 4ajsC 1ai2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P08200, isocitrate dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 131 molecules
#2: Chemical | ChemComp-NMN / |
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#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-AKG / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEEREDNonpolymer details | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP): THIS IS NADPH, THE REDUCED FORM OF NADP ...NADP NICOTINAMI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 1.85 M 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9535 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Details: TOROIDAL MIRROR |
Radiation | Monochromator: CHANNEL-CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9535 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→60 Å / Num. obs: 23556 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 47.08 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.69→2.85 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.8 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AI2 Resolution: 2.687→52.894 Å / SU ML: 0.66 / σ(F): 1.99 / Phase error: 18.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.034 Å2 / ksol: 0.396 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.687→52.894 Å
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Refine LS restraints |
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LS refinement shell |
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