1KX5

X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution

Structural Biology Knowledgebase: 1KX5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.208

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KX5

Classification: STRUCTURAL PROTEIN / DNA

Total Structure Weight: 200284.54


Macromolecule Entities
Molecule Chains Length Organism Details
histone H3 A, E 135 Xenopus laevis Mutation: G102A
Gene Name(s):
histone H4 B, F 102 Xenopus laevis Gene Name(s):
histone H2A.1 C, G 128 Xenopus laevis Mutation: G99R, A123S, ΔA126
Gene Name(s):
histone H2B.2 D, H 125 Xenopus laevis Mutation: S29T
Gene Name(s):
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'(ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGAATCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT)3') I 147 Homo sapiens palindromic 147 base pair DNA duplex with exception of position 0
DNA (5'(ATCAATATCCACCTGCAGATACTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCTGGATTCCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGTATCTGCAGGTGGATATTGAT)3') J 147 Homo sapiens palindromic 147 base pair DNA duplex with exception of position 0

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.208
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 105.95 α = 90.00
b = 181.17 β = 90.00
c = 109.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-31
  • Released Date: 2002-12-25
  • Deposition author(s): Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W., Richmond, T.J.

Revision History

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