4FT8 | pdb_00004ft8

E. coli Catabolite Activator Protein with Cobalt and Sulfate Ligands

• PDB DOI: https://doi.org/10.2210/pdb4FT8/pdb

• Classification: TRANSCRIPTION ACTIVATOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-27 Released: 2013-12-18 
• Deposition Author(s): Rao, R., Lawson, C.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of catabolite activator protein with cobalt(II) and sulfate.

Rao, R.R., Lawson, C.L.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 560-563

• PubMed: 24817710 
• DOI: https://doi.org/10.1107/S2053230X14005366
• Primary Citation Related Structures: 
  4FT8


• PubMed Abstract: 
  

  The crystal structure of cyclic AMP-catabolite activator protein (CAP) from Escherichia coli containing cobalt(II) chloride and ammonium sulfate is reported at 1.97 Å resolution. Each of the two CAP subunits in the asymmetric unit binds one cobalt(II) ion, in each case coordinated by N-terminal domain residues His19, His21 and Glu96 plus an additional acidic residue contributed via a crystal contact. The three identified N-terminal domain cobalt-binding residues are part of a region of CAP that is important for transcription activation at class II CAP-dependent promoters. Sulfate anions mediate additional crystal lattice contacts and occupy sites corresponding to DNA backbone phosphate positions in CAP-DNA complex structures.

---

Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.

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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.11 kDa 
• Atom Count: 3,784 
• Modeled Residue Count: 400 
• Deposited Residue Count: 418 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catabolite gene activator	A, B	209	Escherichia coli K-12	Mutation(s): 0  Gene Names: b3357, cap, crp, csm, JW5702
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12)) Explore P0ACJ8  Go to UniProtKB:  P0ACJ8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	C [auth A], K [auth B]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	J [auth A], S [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.143	α = 90
b = 108.452	β = 90
c = 44.32	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Rao, R., Lawson, C.L.

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2014-05-07
  Changes: Database references
• Version 1.2: 2014-09-24
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description