2NYI

Crystal Structure of an Unknown Protein from Galdieria sulphuraria

• PDB DOI: https://doi.org/10.2210/pdb2NYI/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Galdieria sulphuraria
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-20 Released: 2006-12-12 
• Deposition Author(s): Bitto, E., Wesenberg, G.E., Phillips Jr., G.N., McCoy, J.G., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.214 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Literature

Crystal structure of tandem ACT domain-containing protein ACTP from Galdieria sulphuraria.

Bitto, E., Kim, D.J., Bingman, C.A., Kim, H.J., Han, B.W., Phillips, G.N.

(2012) Proteins 80: 2105-2109

• PubMed: 22528523 
• DOI: https://doi.org/10.1002/prot.24101
• Primary Citation of Related Structures:  
  2NYI


• PubMed Abstract: 
  

  The ACT domain is a structurally conserved small molecule binding domain which is mostly involved in amino acid and purine metabolism. Here, we report the crystal structure of a tandem ACT domain-containing protein (ACTP) from Galdieria sulphuraria. The two ACTP monomers in the asymmetric unit form a dimer with a non-crystallographic twofold axis in a domain-swapped manner, showing a horseshoe-like structure with a central crevice. This structure contributes to expand our knowledge on the structural diversity of ACT domain-containing proteins.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Georgian Court University, Lakewood, New Jersey 08701, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 42.42 kDa 
• Atom Count: 3,014 
• Modelled Residue Count: 341 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown protein	A, B	195	Galdieria sulphuraria	Mutation(s): 0  Gene Names: c855_101305g34.t1(MSU_Galdi)
UniProt
Find proteins for J3QW32 (Galdieria sulphuraria) Explore J3QW32  Go to UniProtKB:  J3QW32

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.214 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.013	α = 90
b = 79.991	β = 111.25
c = 55.53	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Bitto, E., Wesenberg, G.E., Phillips Jr., G.N., McCoy, J.G., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-07-25
  Changes: Database references
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2024-11-13
  Changes: Structure summary