3UGV | pdb_00003ugv

Crystal structure of an enolase from alpha pretobacterium bal199 (EFI TARGET EFI-501650) with bound MG

• PDB DOI: https://doi.org/10.2210/pdb3UGV/pdb

• Classification: LYASE
• Organism(s): alpha proteobacterium BAL199
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-03 Released: 2011-11-23 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.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: 2.30 Å
• R-Value Free: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an enolase from alpha pretobacterium bal199 (EFI TARGET EFI-501650) with bound MG

Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., 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: 344.12 kDa 
• Atom Count: 23,260 
• Modeled Residue Count: 2,905 
• Deposited Residue Count: 3,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase	A, B, C, D, E, F, G, H	390	alpha proteobacterium BAL199	Mutation(s): 0  Gene Names: BAL199_22462
UniProt
Find proteins for A0ACD6B9K3 (alpha proteobacterium BAL199) Explore A0ACD6B9K3  Go to UniProtKB:  A0ACD6B9K3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	L [auth A], Y [auth F]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	K [auth A], O [auth B], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	AA [auth G], BA [auth H], CA [auth H], I [auth A], J [auth A], M [auth B], N [auth B], P [auth C], Q [auth C], R [auth D], S [auth D], U [auth E], V [auth E], W [auth F], X [auth F], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.711	α = 90
b = 152.984	β = 90
c = 173.535	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: 2011-11-23 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Hillerich, B., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2011-11-23
  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