1J59 | pdb_00001j59

CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1J59/pdb
• Entry: 1J59 supersedes: 1BER
• NAKB: 1J59

• Classification: GENE REGULATION/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-03-01 Released: 2002-03-01 
• Deposition Author(s): Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y.W., Ebright, R.H., Berman, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.279 (Depositor) 
• R-Value Work: 
  0.199 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface.

Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y.W., Ebright, R.E., Berman, H.M.

(1996) J Mol Biology 260: 395-408

• PubMed: 8757802 
• DOI: https://doi.org/10.1006/jmbi.1996.0409
• Primary Citation Related Structures: 
  1J59


• PubMed Abstract: 
  

  The crystallographic structure of the CAP-DNA complex at 3.0 A resolution has been reported previously. For technical reasons, the reported structure had been determined using a gapped DNA molecule lacking two phosphates important for CAP-DNA interaction. In this work, we report the crystallographic structure of the CAP-DNA complex at 2.5 A resolution using a DNA molecule having all phosphates important for CAP-DNA interaction. The present resolution permits unambiguous identification of amino acid-base and amino acid-phosphate hydrogen bonded contacts in the CAP-DNA complex. In addition, the present resolution permits accurate definition of the kinked DNA conformation in the CAP-DNA complex.

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Organizational Affiliation: 
• Department of Chemistry and The Waksman Institute, Rutgers University, New Brunswick, NJ 08855-0939, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.75 kDa 
• Atom Count: 4,718 
• Modeled Residue Count: 458 
• Deposited Residue Count: 480 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CATABOLITE GENE ACTIVATOR PROTEIN (CAP)	E [auth A], F [auth B]	209	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12)) Explore P0ACJ8  Go to UniProtKB:  P0ACJ8

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*C)-3'	A [auth C], C [auth E]	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*AP*TP*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G )-3'	B [auth D], D [auth F]	17	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	G [auth A], H [auth B]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.279 (Depositor) 
• R-Value Work:  0.199 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.99	α = 90
b = 152.8	β = 90
c = 76.06	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-01 
Deposition Author(s): Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y.W., Ebright, R.H., Berman, H.M.
• This entry supersedes: 1BER

Revision History  

• Version 1.0: 2002-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations