1EQZ

X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION

Structural Biology Knowledgebase: 1EQZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.219

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1EQZ

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 200893.25


Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (HISTONE H2A) A, E 129 Gallus gallus Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER
Gene Name(s):
PROTEIN (HISTONE H2B) B, F 126 Gallus gallus Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER
Gene Name(s): H2B-VII
PROTEIN (HISTONE H3) C, G 136 Gallus gallus Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER
Gene Name(s): H3-I H3-II H3-III H3-IV H3-V H3-VI H3-VII H3-VIII
PROTEIN (HISTONE H4) D, H 103 Gallus gallus Details: SUBUNIT OF SALT-EXTRACTED HISTONE OCTAMER
Gene Name(s): H4-I H4-II H4-III H4-IV H4-V H4-VI H4-VII
Macromolecule Entities
Molecule Chains Length Organism Details
146 NUCLEOTIDES LONG DNA I, J 146 synthetic ENDS MUTATED TO ECO RV COMPATIBLE BLUNT ENDS AND ECO RI LINKER ADDED AT ALU I SITE OF 5' HALF OF NATIVE NUCLEOSOME FRAGMENT

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CAC
Query on CAC

G CACODYLATE ION
dimethylarsinate (Synonym)
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

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

I, J POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, E CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.219
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 105.28 α = 90.00
b = 109.71 β = 90.00
c = 181.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-04-06
  • Released Date: 2000-04-17
  • Deposition author(s): Hanson, B.L., Harp, J.M., Timm, D.E., Bunick, G.J.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4