3WLX | pdb_00003wlx

Crystal structure of low-specificity L-threonine aldolase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb3WLX/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-15 Released: 2014-12-17 
• Deposition Author(s): Qin, H.-M., Imai, F.L., Miyakawa, T., Kataoka, M., Okai, M., Hou, F., Ohtsuka, J., Nagata, K., Shimizu, S., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Structure analysis of L-threonine aldolase from Escherichia coli unravels the low-specificity and thermostability

Qin, H.-M., Imai, F.L., Miyakawa, T., Kataoka, M., Okai, M., Ohtsuka, J., Hou, F., Nagata, K., Shimizu, S., Tanokura, M.

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: 73.69 kDa 
• Atom Count: 5,303 
• Modeled Residue Count: 663 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low specificity L-threonine aldolase	A [auth B], B [auth A]	333	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0870, JW0854, ltaE, ybjU EC: 4.1.2.48
UniProt
Find proteins for P75823 (Escherichia coli (strain K12)) Explore P75823  Go to UniProtKB:  P75823

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLG	C [auth B], D [auth A]	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] C10 H15 N2 O7 P FEVQWBMNLWUBTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.73	α = 90
b = 100.34	β = 90
c = 174.62	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Qin, H.-M., Imai, F.L., Miyakawa, T., Kataoka, M., Okai, M., Hou, F., Ohtsuka, J., Nagata, K., Shimizu, S., Tanokura, M.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description