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- PDB-1ika: STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT... -

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Entry
Database: PDB / ID: 1ika
TitleSTRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE
ComponentsISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(NAD(A)-CHOH(D))
Function / homologyIsocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate and isopropylmalate dehydrogenases signature. / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / electron transport chain / tricarboxylic acid cycle ...Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate and isopropylmalate dehydrogenases signature. / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / electron transport chain / tricarboxylic acid cycle / NAD binding / response to oxidative stress / magnesium ion binding / cytosol / cytoplasm / Isocitrate dehydrogenase [NADP]
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / 2.7 Å resolution
AuthorsStoddard, B.L. / Koshland Junior, D.E.
Citation
Journal: Biochemistry / Year: 1993
Title: Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrate.
Authors: Stoddard, B.L. / Koshland Jr., D.E.
#1: Journal: Biochemistry / Year: 1993
Title: The Structure of Isocitrate Dehydrogenase with Isocitrate, Nadp, and Calcium at 2.5 Angstroms Resolution: A Pseudo-Michaelis Ternary Complex
Authors: Stoddard, B.L. / Dean, A. / Koshland Junior, D.E.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 15, 1993 / Release: Jul 31, 1994
RevisionDateData content typeGroupProviderType
1.0Jul 31, 1994Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9963
Polyers45,8101
Non-polymers1862
Water0
1
A: ISOCITRATE DEHYDROGENASE
hetero molecules

A: ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9916
Polyers91,6192
Non-polymers3724
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area (Å2)7920
ΔGint (kcal/M)-66
Surface area (Å2)32040
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)105.100, 105.100, 150.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP 43 21 2
Atom site foot note1: ARG 112 - SER 113 OMEGA = 210.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLY 261 - PRO 262 OMEGA = 237.15 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein/peptide ISOCITRATE DEHYDROGENASE /


Mass: 45809.562 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Formula: C5H6O5 / Alpha-Ketoglutaric acid

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.53 / Density percent sol: 72.84 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
120 mg/mlprotein1drop
240 %satammonium sulfate1drop
3ammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.7 Å / Number obs: 14729 / Rmerge I obs: 0.108 / Observed criterion sigma I: 2

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
Least-squares processR factor R work: 0.185 / R factor obs: 0.185 / Highest resolution: 2.7 Å / Lowest resolution: 3 Å / Number reflection obs: 14729
Refine hist #LASTHighest resolution: 2.7 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 3196 / Nucleic acid: 0 / Ligand: 11 / Solvent: 0 / Total: 3207
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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