4UEG | pdb_00004ueg

Crystal structure of human glycogenin-2 catalytic domain

• PDB DOI: https://doi.org/10.2210/pdb4UEG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-12-17 Released: 2014-12-24 
• Deposition Author(s): Fairhead, M., Strain-Damerell, C., Krojer, T., Froese, D.S., Kopec, J., Nowak, R., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Glycogenin-2 Catalytic Domain

Fairhead, M., Strain-Damerell, C., Krojer, T., Froese, D.S., Kopec, J., Nowak, R., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 66.25 kDa 
• Atom Count: 4,217 
• Modeled Residue Count: 491 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOGENIN-2	A, B	288	Homo sapiens	Mutation(s): 2  EC: 2.4.1.186
UniProt & NIH Common Fund Data Resources
Find proteins for O15488 (Homo sapiens) Explore O15488  Go to UniProtKB:  O15488
PHAROS:  O15488 GTEx:  ENSG00000056998

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.113	α = 90
b = 80.541	β = 118.74
c = 73.683	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Fairhead, M., Strain-Damerell, C., Krojer, T., Froese, D.S., Kopec, J., Nowak, R., Burgess-Brown, N., von Delft, F., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description