3lja

X-ray diffraction
2.75Å resolution

Using Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome

Released:
Source organism: Xenopus laevis
Primary publication:
Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome.
J. Mol. Biol. 398 633-40 (2010)
PMID: 20350553

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Structure domains: Histone, subunit A
147mer DNA Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.37 KDa
147mer DNA Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.36 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 106.348Å b: 109.785Å c: 182.424Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.222 0.259
Expression system: Escherichia coli