1VB3 | pdb_00001vb3

Crystal Structure of Threonine Synthase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb1VB3/pdb

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


• Deposited: 2004-02-21 Released: 2005-06-21 
• Deposition Author(s): Omi, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.220 (DCC) 

Literature

Crystal Structure of Threonine Synthase from Escherichia coli

Omi, R., Goto, M., Miyahara, I., Mizuguchi, H., Hayashi, H., Kagamiyama, H., Hirotsu, K.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 47.45 kDa 
• Atom Count: 3,522 
• Modeled Residue Count: 428 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine synthase	A	428	Escherichia coli	Mutation(s): 0  EC: 4.2.3.1
UniProt
Find proteins for P00934 (Escherichia coli (strain K12)) Explore P00934  Go to UniProtKB:  P00934

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KPA	C [auth A]	2-OXO-5-PHOSPHONOPENTANOIC ACID C5 H9 O6 P UFXCSKVWNXIICO-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.220 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.931	α = 90
b = 86.931	β = 90
c = 141.331	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-21 
Deposition Author(s): Omi, R.

Revision History  

• Version 1.0: 2005-06-21
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations