5MUX | pdb_00005mux

Crystal structure of 2-methylcitrate dehydratase (MmgE) from Bacillus subtilis.

• PDB DOI: https://doi.org/10.2210/pdb5MUX/pdb

• Classification: LYASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-14 Released: 2018-02-14 
• Deposition Author(s): Baker, G.E., Race, P.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Crystal structure of 2-methylcitrate dehydratase (MmgE) from Bacillus subtilis.

Baker, G.E., Race, P.R.

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 and generated by PISA (software)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 318.76 kDa 
• Atom Count: 23,106 
• Modeled Residue Count: 2,824 
• Deposited Residue Count: 2,832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-methylcitrate dehydratase	A, B, C, D, E, F	472	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: prpD, mmgE, yqiP, BSU24130 EC: 4.2.1.79 (PDB Primary Data), 4.2.1.3 (PDB Primary Data), 4.2.1 (UniProt)
UniProt
Find proteins for P45859 (Bacillus subtilis (strain 168)) Explore P45859  Go to UniProtKB:  P45859

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.831	α = 90
b = 194.409	β = 92.74
c = 90.869	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Baker, G.E., Race, P.R.

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Refinement description