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- PDB-1idf: ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME -

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Basic information

Entry
Database: PDB / ID: 1idf
TitleISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME
ComponentsISOCITRATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (NAD(A)-CHOH(D))
Function / homology
Function and homology information


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
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBolduc, J.M. / Dyer, D.H. / Scott, W.G. / Singer, P. / Sweet, R.M. / Koshland Junior, D.E. / Stoddard, B.L.
Citation
Journal: Science / Year: 1995
Title: Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase.
Authors: Bolduc, J.M. / Dyer, D.H. / Scott, W.G. / Singer, P. / Sweet, R.M. / Koshland Jr., D.E. / Stoddard, B.L.
#1: Journal: Biochemistry / Year: 1991
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 Junior, D.E. / Stroud, R.M.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Regulation of Isocitrate Dehydrogenase by Phosphorylation Involves No Long-Range Conformational Change in the Free Enzyme
Authors: Hurley, J.H. / Dean, A.M. / Thorsness, P.E. / Koshland Junior, D.E. / Stroud, R.M.
#3: Journal: Science / Year: 1990
Title: Regulation of an Enzyme by Phosphorylation at the Active Site
Authors: Hurley, J.H. / Dean, A.M. / Sohl, J.L. / Koshland Junior, D.E. / Stroud, R.M.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Structure of a Bacterial Enzyme Regulated by Phosphorylation, Isocitrate Dehydrogenase
Authors: Hurley, J.H. / Thorsness, P.E. / Ramalingam, V. / Helmers, N.H. / Koshland Junior, D.E. / Stroud, R.M.
History
DepositionJan 18, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOCITRATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)45,8121
Polymers45,8121
Non-polymers00
Water00
1
A: ISOCITRATE DEHYDROGENASE

A: ISOCITRATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)91,6232
Polymers91,6232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6550 Å2
ΔGint-44 kcal/mol
Surface area33840 Å2
MethodPISA, PQS
Unit cell
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-MP43212
Atom site foot note1: CIS PROLINE - PRO 262

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Components

#1: Protein ISOCITRATE DEHYDROGENASE / IDH


Mass: 45811.578 Da / Num. of mol.: 1 / Mutation: K230M
Source method: isolated from a genetically manipulated source
Details: APO ENZYME / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JLK1 / Gene: ICD / Variant: ICD(-) (DEFICIENT IN WT IDH GENE) / Plasmid: PTK513 / Gene (production host): ICD
Production host: PEMBL (DENTE ET AL 1983 NUC ACIDS RES 11,1645)
References: UniProt: P08200, isocitrate dehydrogenase (NADP+)

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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 Å3/Da / Density % sol: 72.84 %
Description: THE MERGING R VALUE GIVEN HERE IS CRYSTAL TO CRYSTAL. THE MERGING R VALUE FOR INDIVIDUAL CRYSTALS IS 0.068, 0.072. DATA WAS COLLECTED FROM TWO SEPARATE CRYSTALS AND MERGED TOGETHER WITH PROTSYS.
Crystal
*PLUS
Density % sol: 73 %
Crystal grow
*PLUS
pH: 5.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
128 mg/mldephosphorylated IDH1reservoir
234 %satammonium sulfate1reservoir
3100 mM1reservoirNaCl
435 mM1reservoirNa2HPO4
59 mMcitric acid1reservoir
60.2 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 6, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 24707 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.095
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Rmerge(I) obs: 0.095

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
MSCdata reduction
X-PLOR3.1phasing
RefinementHighest resolution: 2.5 Å / σ(F): 2
RfactorNum. reflection
Rfree0.262 -
Rwork0.223 -
obs0.223 22061
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 0 0 3195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
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_deg4.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.69
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.608
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.69
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.608

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