5J04 | pdb_00005j04

Crystal structure of Enolase from Synechococcus elongatus, complex with phosphoenolpyruvate

• PDB DOI: https://doi.org/10.2210/pdb5J04/pdb

• Classification: LYASE
• Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-26 Released: 2016-04-20 
• Deposition Author(s): Gonzalez, J.M.
• Funding Organization(s): National Scientific and Technical Research Council (CONICET)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

The structure of Synechococcus elongatus enolase reveals key aspects of phosphoenolpyruvate binding

Gonzalez, J.M., Marti-Arbona, R., Chen, J.C.-H., Unkefer, C.J.

(2022) Acta Crystallogr F Struct Biol Commun F78: 177-184

• DOI: https://doi.org/10.1107/S2053230X22003612

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.23 kDa 
• Atom Count: 6,504 
• Modeled Residue Count: 848 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enolase	A, B	424	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0  Gene Names: eno, Synpcc7942_0639 EC: 4.2.1.11
UniProt
Find proteins for Q31QJ8 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31QJ8  Go to UniProtKB:  Q31QJ8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEP (Subject of Investigation/LOI)	C [auth A], I [auth B]	PHOSPHOENOLPYRUVATE C3 H5 O6 P DTBNBXWJWCWCIK-UHFFFAOYSA-N
ACT	H [auth A], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.23	α = 90
b = 164.23	β = 90
c = 72.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Gonzalez, J.M.

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Funding Organization	Location	Grant Number
National Scientific and Technical Research Council (CONICET)	Argentina	PIP0024

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 2.0: 2022-04-13
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Refinement description
• Version 2.2: 2024-02-28
  Changes: Database references, Source and taxonomy