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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.245 (Depositor), 0.251 (DCC)
R-Value Work:
0.213 (Depositor), 0.223 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

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

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q31QJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEP (Subject of Investigation/LOI) Query on PEP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	PHOSPHOENOLPYRUVATE C₃ H₅ O₆ P DTBNBXWJWCWCIK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	H [auth A], M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] J [auth B] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.245 (Depositor), 0.251 (DCC)
R-Value Work: 0.213 (Depositor), 0.223 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-04-20

Deposition Author(s):

Gonzalez, J.M.

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

Revision History (Full details and data files)

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

5J04 | pdb_00005j04

Crystal structure of Enolase from Synechococcus elongatus, complex with phosphoenolpyruvate

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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