5ONW

X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 5ONW

Classification: DNA BINDING PROTEIN

Total Structure Weight: 200300.39


Macromolecule Entities
Molecule Chains Length Organism Details
Histone H3.2 A, E 135 Xenopus laevis Mutation: R40C, G102A, C110A
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B, F 103 Xenopus laevis Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2A C, G 129 Xenopus laevis Mutation: N38C
Gene Name(s): hist1h2aj LOC494591
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2B 1.1 D, H 122 Xenopus laevis Mutation: S29T
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (147-MER) I 147 Homo sapiens
DNA (147-MER) J 147 Homo sapiens

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MN
Query on MN

D, E, I, J MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, C, E, G CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
G47
Query on G47
I, J DNA LINKING C12 H18 N5 O7 P S DG

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.208
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 106.56 α = 90.00
b = 183.83 β = 90.00
c = 109.49 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-08-04
  • Released Date: 2017-11-22
  • Deposition author(s): Frouws, T.D., Barth, P.D., Richmond, T.J.

Revision History

  • Version 1_0: 2017-11-22

    Type: Initial release