3GEB | pdb_00003geb

Crystal Structure of edeya2

• PDB DOI: https://doi.org/10.2210/pdb3GEB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-25 Released: 2009-04-07 
• Deposition Author(s): Kim, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Structure of edeya2

Kim, S.J., Jeong, D.G., Jung, S.K., Seong, E.R.

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 and generated by PISA (software)

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.31 kDa 
• Atom Count: 8,355 
• Modeled Residue Count: 1,025 
• Deposited Residue Count: 1,096 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eyes absent homolog 2	A, B, C, D	274	Homo sapiens	Mutation(s): 0  EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for O00167 (Homo sapiens) Explore O00167  Go to UniProtKB:  O00167
PHAROS:  O00167 GTEx:  ENSG00000064655

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.612	α = 90
b = 183.612	β = 90
c = 120.15	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SOLVE	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Kim, S.J.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations