8XU1 | pdb_00008xu1

DaCS-oxaloacetate complex

• PDB DOI: https://doi.org/10.2210/pdb8XU1/pdb

• Classification: TRANSFERASE
• Organism(s): Desulfurella acetivorans A63
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-12 Released: 2025-01-22 
• Deposition Author(s): Yang, L., Fang, Y.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: in silico

Literature

DaCS-oxaloacetate complex

Yang, L., Fang, Y.J.

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 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)

Macromolecule Content 

• Total Structure Weight: 147.17 kDa 
• Atom Count: 10,421 
• Modeled Residue Count: 1,302 
• Deposited Residue Count: 1,305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
citrate synthase	A, B, C	435	Desulfurella acetivorans A63	Mutation(s): 19  EC: 2.3.3.16
UniProt
Find proteins for A0A7C6A739 (Desulfurella acetivorans) Explore A0A7C6A739  Go to UniProtKB:  A0A7C6A739

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAA (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	OXALOACETATE ION C4 H3 O5 KHPXUQMNIQBQEV-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.1	α = 90
b = 111.28	β = 116.07
c = 99.56	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Yang, L., Fang, Y.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release