4F4F | pdb_00004f4f

X-Ray crystal structure of PLP bound Threonine synthase from Brucella melitensis

• PDB DOI: https://doi.org/10.2210/pdb4F4F/pdb

• Classification: LYASE
• Organism(s): Brucella melitensis bv. 1 str. 16M
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-10 Released: 2012-06-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

X-Ray crystal structure of PLP bound Threonine synthase from Brucella melitensis

Christensen, J.S., Fairman, J.W., Staker, B.L., Stewart, L.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.64 kDa 
• Atom Count: 7,571 
• Modeled Residue Count: 928 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Threonine synthase	A, B	468	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0  Gene Names: BMEI1450, BAWG_0773 EC: 4.2.3.1
UniProt
Find proteins for Q8YFS0 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YFS0  Go to UniProtKB:  Q8YFS0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34F4F

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.99	α = 90
b = 100.01	β = 91.29
c = 92.13	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2020-01-15
  Changes: Advisory, Database references, Derived calculations
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2025-10-22
  Changes: Structure summary