4UML | pdb_00004uml

Crystal structure of ganglioside induced differentiation associated protein 2 (GDAP2) macro domain

• PDB DOI: https://doi.org/10.2210/pdb4UML/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-05-19 Released: 2014-05-28 
• Deposition Author(s): Elkins, J.M., Wang, J., Kopec, J., Wang, D., Strain-Damerell, C., Shrestha, L., Sieg, C., Tallant, C., Newman, J.A., von Delft, F., Bountra, C., Edwards, A., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of Gdap2

Elkins, J.M., Wang, J., Knapp, S.

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)

Macromolecule Content 

• Total Structure Weight: 25.53 kDa 
• Atom Count: 1,677 
• Modeled Residue Count: 201 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GANGLIOSIDE-INDUCED DIFFERENTIATION-ASSOCIATED PROTEIN 2	A	229	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXN4 (Homo sapiens) Explore Q9NXN4  Go to UniProtKB:  Q9NXN4
PHAROS:  Q9NXN4 GTEx:  ENSG00000196505

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.84	α = 90
b = 70.84	β = 90
c = 97.549	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-28 
Deposition Author(s): Elkins, J.M., Wang, J., Kopec, J., Wang, D., Strain-Damerell, C., Shrestha, L., Sieg, C., Tallant, C., Newman, J.A., von Delft, F., Bountra, C., Edwards, A., Knapp, S.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description