1JG8 | pdb_00001jg8

Crystal Structure of Threonine Aldolase (Low-specificity)

• PDB DOI: https://doi.org/10.2210/pdb1JG8/pdb

• Classification: LYASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-06-23 Released: 2001-07-04 
• Deposition Author(s): Kielkopf, C.L., Bonanno, J., Ray, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.222 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal Structure of Low-specificity Threonine Aldolase, a Key Enzyme in Glycine Biosynthesis

Kielkopf, C.L., Bonanno, J., Ray, S., Burley, S.K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (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: 153.4 kDa 
• Atom Count: 11,435 
• Modeled Residue Count: 1,370 
• Deposited Residue Count: 1,388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-allo-threonine aldolase	A, B, C, D	347	Thermotoga maritima	Mutation(s): 1  Gene Names: TM1744 EC: 4.1.2.5
UniProt
Find proteins for Q9X266 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X266  Go to UniProtKB:  Q9X266

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], G [auth B], H [auth B], I [auth C], K [auth D], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth A], J [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.222 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.89	α = 90
b = 100.6	β = 90
c = 149.82	γ = 90

Software Package:

Software Name	Purpose
SnB	phasing
MLPHARE	phasing
DM	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-04 
Deposition Author(s): Kielkopf, C.L., Bonanno, J., Ray, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2001-07-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2025-03-26
  Changes: Data collection, Database references, Structure summary