8XU2 | pdb_00008xu2

DaCS-citrate complex

• PDB DOI: https://doi.org/10.2210/pdb8XU2/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.Y., 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: 2.19 Å
• R-Value Free: 
  0.203 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

DaCS-citrate complex

Yang, L.Y., 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)

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)

Macromolecule Content

• Total Structure Weight: 395.13 kDa 
• Atom Count: 29,116 
• Modelled Residue Count: 3,483 
• Deposited Residue Count: 3,504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
citrate synthase	A, B, C, D, E, F, G, H	438	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
CIT (Subject of Investigation/LOI)	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.203 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 362.335	α = 90
b = 362.335	β = 90
c = 77.886	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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