4MTJ | pdb_00004mtj

Structure of the b12-independent glycerol dehydratase with 1,2-propanediol bound

• PDB DOI: https://doi.org/10.2210/pdb4MTJ/pdb
• Entry: 4MTJ supersedes: 1R9E

• Classification: HYDROLASE
• Organism(s): Clostridium butyricum
• Mutation(s): No 


• Deposited: 2013-09-19 Released: 2013-10-09 
• Deposition Author(s): LaMattina, J., Wright, A.V., Demick, J., Soucaille, P., Lanzilotta, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

When Computational Chemistry and Modern Software Get It Right; New Insight Into the Mechanism of a Glycyl Radical Enzyme

LaMattina, J., Wright, A.V., Demick, J., Soucaille, P., Lanzilotta, W.N.

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)

Macromolecule Content 

• Total Structure Weight: 176.46 kDa 
• Atom Count: 13,286 
• Modeled Residue Count: 1,572 
• Deposited Residue Count: 1,574 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B12-independent glycerol dehydratase	A, B	787	Clostridium butyricum	Mutation(s): 0  Gene Names: dhaB1
UniProt
Find proteins for Q8GEZ8 (Clostridium butyricum) Explore Q8GEZ8  Go to UniProtKB:  Q8GEZ8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGO	C [auth A], D [auth B]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.696	α = 90
b = 212.399	β = 90
c = 198.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): LaMattina, J., Wright, A.V., Demick, J., Soucaille, P., Lanzilotta, W.N.
• This entry supersedes: 1R9E

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description