6UM4 | pdb_00006um4

Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863

• PDB DOI: https://doi.org/10.2210/pdb6UM4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Naegleria fowleri
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-10-09 Released: 2019-10-23 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 587.41 kDa 
• Atom Count: 31,359 
• Modeled Residue Count: 3,908 
• Deposited Residue Count: 5,328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase	A, B, C, D, E, F, G, H, I, J, K, L	444	Naegleria fowleri	Mutation(s): 0  Gene Names: mRNA1_NF0021050 EC: 1.1.1.37
UniProt
Find proteins for A0A5S8WFA9 (Naegleria fowleri) Explore A0A5S8WFA9  Go to UniProtKB:  A0A5S8WFA9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	M [auth D], N [auth J], O [auth J], P [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36um4

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.33	α = 91.093
b = 137.48	β = 89.998
c = 139.28	γ = 91.482

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing
ARP/wARP	model building
BUCCANEER	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-04-03
  Changes: Refinement description