4DX3

Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502086) from Agrobacterium tumefaciens, with a succinimide residue

• PDB DOI: https://doi.org/10.2210/pdb4DX3/pdb

• Classification: ISOMERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-02-27 Released: 2012-04-18 
• Deposition Author(s): Vetting, M.W., Bouvier, J.T., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., 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: 1.65 Å
• R-Value Free: 0.172 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502086) from Agrobacterium tumefaciens, with a succinimide residue

Vetting, M.W., Bouvier, J.T., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.2 kDa 
• Atom Count: 3,208 
• Modelled Residue Count: 361 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase / muconate lactonizing enzyme family protein	A	400	Agrobacterium fabrum str. C58	Mutation(s): 1  Gene Names: Atu5458 EC: 5.1.2
UniProt
Find proteins for Q7D1T6 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D1T6  Go to UniProtKB:  Q7D1T6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.172 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.54	α = 90
b = 114.54	β = 90
c = 129.06	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Vetting, M.W., Bouvier, J.T., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations