5DBN | pdb_00005dbn

Crystal structure of AtoDA complex

• PDB DOI: https://doi.org/10.2210/pdb5DBN/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli DH5[alpha]
• Expression System: Escherichia coli BL21(DE3), Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-08-21 Released: 2016-08-24 
• Deposition Author(s): Arbing, M.A., Koo, C.W., Shin, A., Medrano-Soto, A., Eisenberg, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AtoDA complex

Arbing, M.A., Koo, C.W., Shin, A., Medrano-Soto, A., Eisenberg, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 191.34 kDa 
• Atom Count: 13,130 
• Modeled Residue Count: 1,711 
• Deposited Residue Count: 1,776 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetate CoA-transferase subunit alpha	A, C, E, G	221	Escherichia coli DH5[alpha]	Mutation(s): 0  Gene Names: atoD, b2221, JW2215 EC: 2.8.3.8
UniProt
Find proteins for P76458 (Escherichia coli (strain K12)) Explore P76458  Go to UniProtKB:  P76458

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetate CoA-transferase subunit beta	B, D, F, H	223	Escherichia coli DH5[alpha]	Mutation(s): 0  Gene Names: atoA, b2222, JW2216 EC: 2.8.3.8
UniProt
Find proteins for P76459 (Escherichia coli (strain K12)) Explore P76459  Go to UniProtKB:  P76459

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	J [auth B], K [auth B], M [auth C], P [auth F], S [auth H]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	I [auth A], L [auth B], O [auth E], R [auth G], T [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	Q [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	N [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.68	α = 90
b = 175.68	β = 113.01
c = 76.16	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Arbing, M.A., Koo, C.W., Shin, A., Medrano-Soto, A., Eisenberg, D.

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description