5B1L

The mouse nucleosome structure containing H3t

Structural Biology Knowledgebase: 5B1L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 5B1L

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 203316.80


Macromolecule Entities
Molecule Chains Length Organism Details
Histone H3t A, E 139 Mus musculus Gene Name(s): Hist1h3a H3a Hist1h3g H3.1-221 H3g Hist1h3h H3.1-291 H3h Hist1h3i H3.1-I H3i
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H4 B, F 106 Mus musculus Gene Name(s): Hist1h4a Hist1h4b H4-53 Hist1h4c H4-12 Hist1h4d Hist1h4f Hist1h4h Hist1h4i Hist1h4j Hist1h4k Hist1h4m Hist2h4a Hist2h4 Hist4h4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2A type 1 C, G 133 Mus musculus Gene Name(s): Hist1h2ab Hist1h2ac Hist1h2ad Hist1h2ae Hist1h2ag Hist1h2ai Hist1h2an Hist1h2ao
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Histone H2B type 3-A D, H 129 Mus musculus Gene Name(s): Hist3h2ba
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (146-MER) I, J 146 Homo sapiens

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

D, 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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.243
  • R-Value Work: 0.197
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 98.97 α = 90.00
b = 107.43 β = 90.00
c = 167.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-12-08
  • Released Date: 2017-02-15
  • Deposition author(s): Urahama, T., Machida, S., Horikoshi, N., Osakabe, A., Tachiwana, H., Taguchi, H., Kurumizaka, H.

Revision History

No revisions since initial release