3PM6

Crystal structure of a putative fructose-1,6-biphosphate aldolase from Coccidioides immitis solved by combined SAD MR

• PDB DOI:  https://doi.org/10.2210/pdb3PM6/pdb

• Classification: LYASE
• Organism(s): Coccidioides immitis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-11-16 Released: 2010-12-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

SAD phasing using iodide ions in a high-throughput structural genomics environment.

Abendroth, J., Gardberg, A.S., Robinson, J.I., Christensen, J.S., Staker, B.L., Myler, P.J., Stewart, L.J., Edwards, T.E.

(2011) J Struct Funct Genomics 12: 83-95

• PubMed: 21359836 
• DOI: https://doi.org/10.1007/s10969-011-9101-7
• Primary Citation of Related Structures:  
  3K9G, 3KM3, 3KW3, 3LUZ, 3MEN, 3NJB, 3O2E, 3OIB, 3P96, 3PFD, 3PM6


• PubMed Abstract: 
  

The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.

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Organizational Affiliation: 

Emerald BioStructures, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 71.78 kDa 
• Atom Count: 4,399 
• Modelled Residue Count: 551 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative fructose-bisphosphate aldolase	A, B	306	Coccidioides immitis	Mutation(s): 0  Gene Names: CIMG_05755 EC: 4.1.2.13
UniProt
Find proteins for P0CJ44 (Coccidioides immitis (strain RS)) Explore P0CJ44  Go to UniProtKB:  P0CJ44

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
ZN	KA [auth B], S [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M33PM6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.91	α = 90
b = 77.77	β = 93.71
c = 68.32	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description