2F0A | pdb_00002f0a

Crystal Structure of Monomeric Uncomplexed form of Xenopus dishevelled PDZ domain

• PDB DOI: https://doi.org/10.2210/pdb2F0A/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-11-12 Released: 2005-11-22 
• Deposition Author(s): Friedland, N., Hung, L.-W., Cheyette, B., Moon, R.T., Earnest, T.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.253 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Conformational flexibility in the PDZ domain of Dishevelled induced by target binding

Friedland, N., Hung, L.-W., Cheyette, B., Miller, J.R., Moon, R.T., Earnest, T.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 6 generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.17 kDa 
• Atom Count: 2,708 
• Modeled Residue Count: 355 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segment polarity protein dishevelled homolog DVL-2	A, B, C, D	98	Xenopus laevis	Mutation(s): 4  Gene Names: dvl2
UniProt
Find proteins for P51142 (Xenopus laevis) Explore P51142  Go to UniProtKB:  P51142

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO	E [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.253 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.834	α = 90
b = 89.834	β = 90
c = 82.471	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Adxv	data processing
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-22 
Deposition Author(s): Friedland, N., Hung, L.-W., Cheyette, B., Moon, R.T., Earnest, T.N.

Revision History  

• Version 1.0: 2005-11-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary