1WSP | pdb_00001wsp

Crystal structure of axin dix domain

• PDB DOI: https://doi.org/10.2210/pdb1WSP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-11-08 Released: 2006-02-14 
• Deposition Author(s): Shibata, N., Hanamura, T., Yamamoto, R., Ueda, Y., Yamamoto, H., Kikuchi, A., Higuchi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.311 (Depositor), 0.315 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Literature

Crystal structure of axin dix domain

Shibata, N., Hanamura, T., Yamamoto, R., Ueda, Y., Yamamoto, H., Kikuchi, A., Higuchi, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.13 kDa 
• Atom Count: 2,273 
• Modeled Residue Count: 251 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Axin 1 protein	A, B, C	84	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for O70239 (Rattus norvegicus) Explore O70239  Go to UniProtKB:  O70239

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
BEZ	G [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.311 (Depositor), 0.315 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.13	α = 90
b = 92.13	β = 90
c = 85.54	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Shibata, N., Hanamura, T., Yamamoto, R., Ueda, Y., Yamamoto, H., Kikuchi, A., Higuchi, Y.

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations