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- PDB-1idc: ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE... -

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Basic information

Entry
Database: PDB / ID: 1idc
TitleISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY
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
2-OXALOSUCCINIC ACID / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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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)46,0263
Polymers45,8121
Non-polymers2142
Water00
1
A: ISOCITRATE DEHYDROGENASE
hetero molecules

A: ISOCITRATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0526
Polymers91,6232
Non-polymers4294
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7860 Å2
ΔGint-59 kcal/mol
Surface area31040 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: RATE-LIMITED ENOLATE INTERMEDIATE / 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+)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OXS / 2-OXALOSUCCINIC ACID


Mass: 190.108 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O7
Has protein modificationN

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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 %
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 sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.7 - 2.1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 1, 1993
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
22.11
ReflectionNum. obs: 17316 / % possible obs: 62 % / Observed criterion σ(I): 1 / Redundancy: 18.7 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 4 Å / % possible obs: 82 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
OXFORDLAUE PACKAGE (J.CAMPBELL)data reduction
X-PLOR3.1phasing
RefinementHighest resolution: 2.5 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rwork0.169 --
obs0.169 17316 -
Rfree--DATA COLLECTED FROM FOUR SEPARATE CRYSTALS AT X26-C (POLYCHROMATIC LAUE BEAM LINE AT BROOKHAVEN NATIONAL LABORATORY) AND MERGED TOGETHER WITH LAUENORM IN OXFORD LAUE DATA REDUCTION PACKAGE.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 14 0 3209
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.661
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.07
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.839
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_deg25.07
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.839

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