8GRV | pdb_00008grv

Dictyostelium discoideum Lactate dehydrogenase (DicLDHA)with NAD

• PDB DOI: https://doi.org/10.2210/pdb8GRV/pdb

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


• Deposited: 2022-09-02 Released: 2022-10-26 
• Deposition Author(s): Dao, O., Lee, K.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Dictyostelium discoideum Lactate dehydrogenase (DicLDHA)

Dao, O., Lee, K.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.95 kDa 
• Atom Count: 2,707 
• Modeled Residue Count: 336 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative D-lactate dehydrogenase	A	366	Dictyostelium discoideum	Mutation(s): 0  Gene Names: ldhA, DDB_G0281101 EC: 1.1.1.28
UniProt
Find proteins for Q54UF7 (Dictyostelium discoideum) Explore Q54UF7  Go to UniProtKB:  Q54UF7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ACT	B [auth A], C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.499	α = 90
b = 104.499	β = 90
c = 163.371	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Dao, O., Lee, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 2.0: 2023-07-12
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2023-11-29
  Changes: Data collection, Refinement description