1ID3

CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS

Structural Biology Knowledgebase: 1ID3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.223

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1ID3

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 200151.74


Macromolecule Entities
Molecule Chains Length Organism Details
HISTONE H3 A, E 135 Saccharomyces cerevisiae Mutation: D123E
Gene Name(s): HHT1 YBR010W YBR0201 HHT2 SIN2 YNL031C N2749
HISTONE H4 B, F 102 Saccharomyces cerevisiae Gene Name(s): HHF1 YBR009C YBR0122 HHF2 YNL030W N2752
HISTONE H2A.1 C, G 131 Saccharomyces cerevisiae Gene Name(s): HTA1 H2A1 SPT11 YDR225W YD9934.10
HISTONE H2B.2 D, H 130 Saccharomyces cerevisiae Gene Name(s): HTB2 H2B2 YBL002W YBL0104
Macromolecule Entities
Molecule Chains Length Organism Details
PALINDROMIC 146BP DNA FRAGMENT I, J 146 Homo sapiens

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MN
Query on MN

C, D, E, G, H, I, J MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.292
  • R-Value Work: 0.223
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.92 α = 90.00
b = 110.40 β = 90.00
c = 192.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-04-03
  • Released Date: 2001-09-28
  • Deposition author(s): White, C.L., Suto, R.K., Luger, K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4