4KEM

Crystal structure of a tartrate dehydratase from azospirillum, target efi-502395, with bound mg and a putative acrylate ion, ordered active site

• PDB DOI: https://doi.org/10.2210/pdb4KEM/pdb

• Classification: LYASE
• Organism(s): Azospirillum sp. B510
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-25 Released: 2013-05-15 
• Deposition Author(s): Vetting, M.W., Wichelecki, D., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Crystal structure of a tartrate dehydratase from azospirillum, target efi-502395, with bound mg and a putative acrylate ion, ordered active site

Vetting, M.W., Wichelecki, D., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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: 86.37 kDa 
• Atom Count: 7,310 
• Modelled Residue Count: 780 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme	A, B	390	Azospirillum sp. B510	Mutation(s): 0  Gene Names: AZL_d02920
UniProt
Find proteins for D3P639 (Azospirillum sp. (strain B510)) Explore D3P639  Go to UniProtKB:  D3P639

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKR	G [auth A], L [auth B]	ACRYLIC ACID C3 H4 O2 NIXOWILDQLNWCW-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.167	α = 90
b = 82.925	β = 100.86
c = 103.266	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Vetting, M.W., Wichelecki, D., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description