1YX2

Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1YX2/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-02-19 Released: 2005-04-05 
• Deposition Author(s): Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.288 
• R-Value Work: 0.212 
• R-Value Observed: 0.219 

Literature

Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis

Kim, Y., Quartey, P., Lezondra, L., Collart, F., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.95 kDa 
• Atom Count: 6,482 
• Modelled Residue Count: 720 
• Deposited Residue Count: 730 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminomethyltransferase	A, B	365	Bacillus subtilis	Mutation(s): 7  Gene Names: gcvT EC: 2.1.2.10
UniProt
Find proteins for P54378 (Bacillus subtilis (strain 168)) Explore P54378  Go to UniProtKB:  P54378

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.288 
• R-Value Work: 0.212 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.628	α = 90
b = 88.095	β = 101.78
c = 88.764	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-05 
Deposition Author(s): Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-04-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary