3SJN | pdb_00003sjn

Crystal structure of enolase Spea_3858 (target EFI-500646) from Shewanella pealeana with magnesium bound

• PDB DOI: https://doi.org/10.2210/pdb3SJN/pdb

• Classification: LYASE
• Organism(s): Shewanella pealeana ATCC 700345
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-21 Released: 2011-07-06 
• Deposition Author(s): Patskovsky, Y., Kim, J., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., 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: 1.90 Å
• R-Value Free: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Enolase Spea_3858 from Shewanella Pealeana

Patskovsky, Y., Kim, J., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Almo, S.C.

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: 82.56 kDa 
• Atom Count: 6,121 
• Modeled Residue Count: 746 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing protein	A, B	374	Shewanella pealeana ATCC 700345	Mutation(s): 0  Gene Names: Spea_3858
UniProt
Find proteins for A8H9D1 (Shewanella pealeana (strain ATCC 700345 / ANG-SQ1)) Explore A8H9D1  Go to UniProtKB:  A8H9D1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL	D [auth A], G [auth B]	Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.207	α = 90
b = 109.207	β = 90
c = 141.034	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-06 
Deposition Author(s): Patskovsky, Y., Kim, J., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., 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: 2011-07-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-03
  Changes: Structure summary
• Version 1.3: 2012-02-22
  Changes: Other, Structure summary
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description