6AJB | pdb_00006ajb

Crystal structure of Trypanosoma brucei glycosomal isocitrate dehydrogenase in complex with NADH, alpha-ketoglutarate and ca2+

• PDB DOI: https://doi.org/10.2210/pdb6AJB/pdb

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


• Deposited: 2018-08-27 Released: 2019-08-28 
• Deposition Author(s): Wang, X., Inaoka, D.K., Shiba, T., Balogun, E.O., Ziebart, N., Allman, S., Watanabe, Y., Nozaki, T., Boshart, M., Bringaud, F., Harada, S., Kita, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.284 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Biochemical characterization of a novel Trypanosoma brucei glycosomal isocitrate dehydrogenase with dual coenzyme specificity (NADP+/NAD+)

Wang, X., Inaoka, D.K., Shiba, T., Balogun, E.O., Ziebart, N., Allman, S., Watanabe, Y., Nozaki, T., Boshart, M., Bringaud, F., Harada, S., Kita, K.

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, gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 190.13 kDa 
• Atom Count: 13,236 
• Modeled Residue Count: 1,641 
• Deposited Residue Count: 1,652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	A, B, C, D	413	Trypanosoma brucei brucei	Mutation(s): 1  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
NAD	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
AKG	L [auth D]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
CA	F [auth A], H [auth B], J [auth C], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.284 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.52	α = 90
b = 70.464	β = 113.42
c = 121.929	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Wang, X., Inaoka, D.K., Shiba, T., Balogun, E.O., Ziebart, N., Allman, S., Watanabe, Y., Nozaki, T., Boshart, M., Bringaud, F., Harada, S., Kita, K.

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description