6VDJ | pdb_00006vdj

Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate and NADH4.

• PDB DOI: https://doi.org/10.2210/pdb6VDJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Apicomplexa sp.
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-12-27 Released: 2020-01-29 
• Deposition Author(s): Theobald, D.L., Wirth, J.D., Classen, S., Perlmutter, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.262 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase

Theobald, D.L., Wirth, J.D., Classen, S., Perlmutter, N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration, fluorescence resonance energy transfer

Macromolecule Content 

• Total Structure Weight: 72.67 kDa 
• Atom Count: 4,837 
• Modeled Residue Count: 625 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lactate dehydrogenase	A, B	330	Apicomplexa sp.	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TXD (Subject of Investigation/LOI)	C [auth A]	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H31 N7 O14 P2 GFDCQHGWOHYWLP-BFAIWXBASA-N
SO4 (Subject of Investigation/LOI)	D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.262 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.695	α = 90
b = 84.695	β = 90
c = 196.007	γ = 120

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: 2020-01-29 
Deposition Author(s): Theobald, D.L., Wirth, J.D., Classen, S., Perlmutter, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM096053

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description