› 1zrd

X-ray diffraction
2.8Å resolution

4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6A;17T]ICAP38 DNA

Released:
DOI: 10.2210/pdb1zrd/pdb
PDB entry 1zrd coloured by chain, front view.
PDB entry 1zrd coloured by chain, side view.
PDB entry 1zrd coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps.
Napoli AA, Lawson CL, Ebright RH, Berman HM
J Mol Biol 357 173-83 (2006)
PMID: 16427082

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114955 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA-binding transcriptional dual regulator CRP Chains: A, B
Molecule details ›
Chains: A, B
Length: 209 amino acids
Theoretical weight: 23.54 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0ACJ8 (Residues: 2-210; Coverage: 100%)
Gene names: JW5702, b3357, cap, crp, csm
Sequence domains:
Structure domains:
5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*AP*GP*AP*T)-3' Chains: W, Y
Molecule details ›
Chains: W, Y
Length: 17 nucleotides
Theoretical weight: 5.26 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*CP*TP*AP*GP*AP*TP*CP*TP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3' Chains: X, Z
Molecule details ›
Chains: X, Z
Length: 21 nucleotides
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CMP 2 x CMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 61.289Å b: 75.345Å c: 178.078Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.28 0.224 0.297
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Murine leukemia virus reverse transcriptase: structural comparison with HIV-1 reverse transcriptase.
Coté et al. (2008)
2 more

2 mentions without citation

Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.
Rodgers et al. (2013)
1 more