4NT4

Crystal structure of the kinase domain of Gilgamesh isoform I from Drosophila melanogaster

• PDB DOI: https://doi.org/10.2210/pdb4NT4/pdb

• Classification: TRANSFERASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-30 Released: 2014-04-09 
• Deposition Author(s): Chen, C.C., Shi, Z.B., Zhou, Z.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.296 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

Structure of the kinase domain of Gilgamesh from Drosophila melanogaster

Han, N., Chen, C., Shi, Z., Cheng, D.

(2014) Acta Crystallogr Sect F Struct Biol Cryst Commun 70: 438-443

• PubMed: 24699734 
• DOI: https://doi.org/10.1107/S2053230X14004774
• Primary Citation of Related Structures:  
  4NT4


• PubMed Abstract: 
  

  The CK1 family kinases regulate multiple cellular aspects and play important roles in Wnt/Wingless and Hedgehog signalling. The kinase domain of Drosophila Gilgamesh isoform I (Gilgamesh-I), a homologue of human CK1-γ, was purified and crystallized. Crystals of methylated Gilgamesh-I kinase domain with a D210A mutation diffracted to 2.85 Å resolution and belonged to space group P43212, with unit-cell parameters a = b = 52.025, c = 291.727 Å. The structure of Gilgamesh-I kinase domain, which was determined by molecular replacement, has conserved catalytic elements and an active conformation. Structural comparison indicates that an extended loop between the α1 helix and the β4 strand exists in the Gilgamesh-I kinase domain. This extended loop may regulate the activity and function of Gilgamesh-I.

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Organizational Affiliation: 

Department of Biology, Qingdao University, Qingdao, Shandong 266021, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.71 kDa 
• Atom Count: 2,360 
• Modelled Residue Count: 300 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gilgamesh, isoform I	A	312	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG6963, Dmel_CG6963, gish EC: 2.7.11 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q86NK8 (Drosophila melanogaster) Explore Q86NK8  Go to UniProtKB:  Q86NK8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.296 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.025	α = 90
b = 52.025	β = 90
c = 291.727	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Chen, C.C., Shi, Z.B., Zhou, Z.C.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2015-03-11
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description