2PPQ | pdb_00002ppq

Crystal structure of the homoserine kinase from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb2PPQ/pdb

• Classification: TRANSFERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2007-04-30 Released: 2007-06-05 
• Deposition Author(s): Zhang, R., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

The crystal structure of the homoserine kinase from Agrobacterium tumefaciens.

Zhang, R., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 36.59 kDa 
• Atom Count: 2,701 
• Modeled Residue Count: 310 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine kinase	A	322	Agrobacterium fabrum str. C58	Mutation(s): 4  Gene Names: thrB, Atu0775, AGR_C_1416 EC: 2.7.1.39
UniProt
Find proteins for Q8UHA8 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q8UHA8  Go to UniProtKB:  Q8UHA8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.338	α = 90
b = 100.619	β = 90
c = 134.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Zhang, R., Xu, X., Zheng, H., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-06-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary