2FEA

Crystal structure of MtnX phosphatase from Bacillus Subtilis at 2.00 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2FEA/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-12-15 Released: 2005-12-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.217 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 

Literature

Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 A resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate.

Xu, Q., Saikatendu, K.S., Krishna, S.S., McMullan, D., Abdubek, P., Agarwalla, S., Ambing, E., Astakhova, T., Axelrod, H.L., Carlton, D., Chiu, H.J., Clayton, T., DiDonato, M., Duan, L., Elsliger, M.A., Feuerhelm, J., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Koesema, E., Miller, M.D., Morse, A.T., Nigoghossian, E., Okach, L., Oommachen, S., Paulsen, J., Reyes, R., Rife, C.L., Schwarzenbacher, R., van den Bedem, H., White, A., Wolf, G., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2007) Proteins 69: 433-439

• PubMed: 17654724 
• DOI: https://doi.org/10.1002/prot.21602
• Primary Citation of Related Structures:  
  2FEA

---

Organizational Affiliation: 

Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, USA.

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: 55.63 kDa 
• Atom Count: 4,061 
• Modelled Residue Count: 450 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase	A, B	236	Bacillus subtilis	Mutation(s): 0  Gene Names: mtnX EC: 3.1.3 (PDB Primary Data), 3.1.3.87 (UniProt)
UniProt
Find proteins for O31667 (Bacillus subtilis (strain 168)) Explore O31667  Go to UniProtKB:  O31667

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.00 Å
• R-Value Free: 0.217 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M32FEA

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.013	α = 90
b = 43.104	β = 98.91
c = 109.553	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-12-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Data collection, Refinement description, Structure summary