2VRF | pdb_00002vrf

CRYSTAL STRUCTURE OF THE HUMAN BETA-2-SYNTROPHIN PDZ DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb2VRF/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-03-31 Released: 2008-04-22 
• Deposition Author(s): Sun, Z., Roos, A.K., Pike, A.C.W., Pilka, E.S., Cooper, C., Elkins, J.M., Murray, J., Arrowsmith, C.H., Doyle, D., Edwards, A., von Delft, F., Bountra, C., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of the Human Beta-2-Syntrophin Pdz Domain

Sun, Z., Roos, A.K., Pike, A.C.W., Pilka, E.S., Cooper, C., Elkins, J.M., Murray, J., Arrowsmith, C.H., Doyle, D., Edwards, A., von Delft, F., Bountra, C., Oppermann, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

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.

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 2-mer - A2 

Biological assembly 5 generated by PQS (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 41.57 kDa 
• Atom Count: 3,034 
• Modeled Residue Count: 380 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2-SYNTROPHIN	A, B, C, D	95	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13425 (Homo sapiens) Explore Q13425  Go to UniProtKB:  Q13425
PHAROS:  Q13425 GTEx:  ENSG00000168807

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.687	α = 90
b = 29.503	β = 95.78
c = 128.382	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Sun, Z., Roos, A.K., Pike, A.C.W., Pilka, E.S., Cooper, C., Elkins, J.M., Murray, J., Arrowsmith, C.H., Doyle, D., Edwards, A., von Delft, F., Bountra, C., Oppermann, U.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-12-05
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description