6CT6 | pdb_00006ct6

Crystal structure of lactate dehydrogenase from Eimeria maxima with NADH and oxamate

• PDB DOI: https://doi.org/10.2210/pdb6CT6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Eimeria maxima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-22 Released: 2019-03-27 
• Deposition Author(s): Wirth, J.D., Xu, C., Theobald, D.L.
• 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: 1.71 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

The Mechanistic, Structural, and Evolutionary Origin of Lactate Dehydrogenase Substrate Specificity in Apicomplexa

Wirth, J.D., Xu, C., Boucher, J.I., Theobald, D.L.

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: homology, gel filtration

Macromolecule Content 

• Total Structure Weight: 75.21 kDa 
• Atom Count: 5,438 
• Modeled Residue Count: 652 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactate dehydrogenase	A, B	338	Eimeria maxima	Mutation(s): 0  Gene Names: EMWEY_00056130
UniProt
Find proteins for U6M598 (Eimeria maxima) Explore U6M598  Go to UniProtKB:  U6M598

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	D [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
GLC	C [auth A], E [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
OXM	F [auth B]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.4	α = 90
b = 83.4	β = 90
c = 227.1	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Wirth, J.D., Xu, C., Theobald, D.L.

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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: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary