7E3N | pdb_00007e3n

Crystal structure of Isocitrate dehydrogenase D252N mutant from Trypanosoma brucei in complexed with NADP+, alpha-ketoglutarate, and ca2+

• PDB DOI: https://doi.org/10.2210/pdb7E3N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-02-09 Released: 2022-02-16 
• Deposition Author(s): Arai, N., Shiba, T., Inaoka, D.K., Kita, K., Wang, X., Otani, M., Matsushiro, S., Kojima, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Isocitrate dehydrogenase from Trypanosoma brucei.

Arai, N., Shiba, T., Inaoka, D.K., Kita, K., Wang, X., Otani, M., Matsushiro, S., Kojima, C.

To be published.

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.77 kDa 
• Atom Count: 3,340 
• Modeled Residue Count: 401 
• Deposited Residue Count: 413 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	A	413	Trypanosoma brucei brucei TREU927	Mutation(s): 2  Gene Names: Tb11.03.0230 EC: 1.1.1.42
UniProt
Find proteins for Q387G0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q387G0  Go to UniProtKB:  Q387G0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
ICT (Subject of Investigation/LOI)	D [auth A]	ISOCITRIC ACID C6 H8 O7 ODBLHEXUDAPZAU-ZAFYKAAXSA-N
CA (Subject of Investigation/LOI)	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.237 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.267	α = 90
b = 89.767	β = 121.04
c = 62.031	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Arai, N., Shiba, T., Inaoka, D.K., Kita, K., Wang, X., Otani, M., Matsushiro, S., Kojima, C.

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description