1IDE | pdb_00001ide

ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE COMPLEX (LAUE DETERMINATION)

• PDB DOI: https://doi.org/10.2210/pdb1IDE/pdb

• Classification: OXIDOREDUCTASE (NAD(A)-CHOH(D))
• Organism(s): Escherichia coli
• Mutation(s): Yes 


• Deposited: 1995-01-18 Released: 1996-03-08 
• Deposition Author(s): Bolduc, J.M., Dyer, D.H., Scott, W.G., Singer, P., Sweet, R.M., Koshland Junior, D.E., Stoddard, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase.

Bolduc, J.M., Dyer, D.H., Scott, W.G., Singer, P., Sweet, R.M., Koshland Jr., D.E., Stoddard, B.L.

(1995) Science 268: 1312-1318

• PubMed: 7761851 
• DOI: https://doi.org/10.1126/science.7761851
• Primary Citation Related Structures: 
  1IDC, 1IDD, 1IDE, 1IDF


• PubMed Abstract: 
  

  Site-directed mutagenesis and Laue diffraction data to 2.5 A resolution were used to solve the structures of two sequential intermediates formed during the catalytic actions of isocitrate dehydrogenase. Both intermediates are distinct from the enzyme-substrate and enzyme-product complexes. Mutation of key catalytic residues changed the rate determining steps so that protein and substrate intermediates within the overall reaction pathway could be visualized.

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Organizational Affiliation: 
• Fred Hutchinson Cancer Research Center, Program in Structural Biology, Seattle, WA 98104, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 46.75 kDa 
• Atom Count: 3,259 
• Modeled Residue Count: 414 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOCITRATE DEHYDROGENASE	A	416	Escherichia coli	Mutation(s): 1  Gene Names: ICD EC: 1.1.1.42
UniProt
Find proteins for P08200 (Escherichia coli (strain K12)) Explore P08200  Go to UniProtKB:  P08200

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ICT	C [auth A]	ISOCITRIC ACID C6 H8 O7 ODBLHEXUDAPZAU-ZAFYKAAXSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.1	α = 90
b = 105.1	β = 90
c = 150.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
OXFORD	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-03-08 
Deposition Author(s): Bolduc, J.M., Dyer, D.H., Scott, W.G., Singer, P., Sweet, R.M., Koshland Junior, D.E., Stoddard, B.L.

Revision History  

• Version 1.0: 1996-03-08
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-07
  Changes: Data collection