4DN1 | pdb_00004dn1

Crystal structure of an ENOLASE (mandelate racemase subgroup member) from Agrobacterium tumefaciens (target EFI-502088) with bound mg and formate

• PDB DOI: https://doi.org/10.2210/pdb4DN1/pdb

• Classification: ISOMERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-08 Released: 2012-03-07 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Bouvier, J.T., Wasserman, S.R., Morisco, L.L., Sojitra, S., Al Obaidi, N.F., 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: 2.05 Å
• R-Value Free: 
  0.194 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an enolase (mandelate racemase subgroup member) from Agrobacterium tumefaciens (target EFI-502088) with bound mg and formate

Vetting, M.W., Toro, R., Bhosle, R., Bouvier, J.T., Wasserman, S.R., Morisco, L.L., Sojitra, S., Al Obaidi, N.F., 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: 89.19 kDa 
• Atom Count: 6,641 
• Modeled Residue Count: 777 
• Deposited Residue Count: 816 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isomerase/lactonizing enzyme	A, B	408	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu5458
UniProt
Find proteins for A9CL63 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CL63  Go to UniProtKB:  A9CL63

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.194 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.36	α = 90
b = 102.36	β = 90
c = 369.62	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Bouvier, J.T., Wasserman, S.R., Morisco, L.L., Sojitra, S., Al Obaidi, N.F., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description