› 5bpd

X-ray diffraction
2.4Å resolution

Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.

Released:
DOI: 10.2210/pdb5bpd/pdb
PDB entry 5bpd coloured by chain, front view.
PDB entry 5bpd coloured by chain, side view.
PDB entry 5bpd coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein.
Ahmad MUD, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W
J Mol Biol 427 3216-3229 (2015)
PMID: 26299937

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118436 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Putative HTH-type transcriptional regulator TrmBL2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 264 amino acids
Theoretical weight: 30.65 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8U3H1 (Residues: 1-264; Coverage: 100%)
Gene names: PF0496, trmBL2
Sequence domains:
Structure domains:
DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)-3') Chain: E
Molecule details ›
Chain: E
Length: 21 nucleotides
Theoretical weight: 6.46 KDa
Source organism: Pyrococcus furiosus
Expression system: Not provided
DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)-3') Chain: F
Molecule details ›
Chain: F
Length: 21 nucleotides
Theoretical weight: 6.42 KDa
Source organism: Pyrococcus furiosus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand GOL 3 x GOL
Ligand IMD 2 x IMD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 95.791Å b: 58.67Å c: 143.074Å
α: 90° β: 92.82° γ: 90°
R-values:
R R work R free
0.236 0.234 0.283
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.
Bender et al. (2016)
3 more