9END

Crystal structure of Methanopyrus kandleri malate dehydrogenase mutant 3

• PDB DOI: https://doi.org/10.2210/pdb9END/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanopyrus kandleri
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-12 Released: 2024-07-10 
• Deposition Author(s): Coquille, S., Roche, J., Girard, E., Madern, D.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.230 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Navigating the conformational landscape of an enzyme. Stabilization of a low populated conformer by evolutionary mutations triggers Allostery into a non-allosteric enzyme.

Coquille, S., Simoes Pereira, C., Brochier-Armanet, C., Roche, J., Santoni, G., Coquelle, N., Girard, E., Sterpone, F., Madern, D.

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.

Biological Assembly Evidence: gel filtration, homology, mass spectrometry

Macromolecule Content

• Total Structure Weight: 70.99 kDa 
• Atom Count: 4,919 
• Modelled Residue Count: 604 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B	317	Methanopyrus kandleri	Mutation(s): 5  Gene Names: HA336_00525
UniProt
Find proteins for Q8TWG5 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore Q8TWG5  Go to UniProtKB:  Q8TWG5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.230 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.82	α = 90
b = 78.82	β = 90
c = 251.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Coquille, S., Roche, J., Girard, E., Madern, D.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-16-CE11-0011
Agence Nationale de la Recherche (ANR)	France	ANR-21-CE44-0034-01

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release