9DAE | pdb_00009dae

Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase

PDB DOI: https://doi.org/10.2210/pdb9DAE/pdb
EM Map EMD-46690: EMDB EMDataResource

Classification: CYTOSOLIC PROTEIN
Organism(s): Staphylothermus marinus F1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-22 Released: 2025-10-29
Deposition Author(s): Legare, S., Kirby, M.W., Stetefeld, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.24 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM Structure of the Multimeric Phosphoenolpyruvate Binding Domain of Staphylothermus marinus Phosphoenolpyruvate Synthase

Legare, S., Kirby, M.W., Stetefeld, J.

To be published.

Macromolecule Content

Total Structure Weight: 2,284.28 kDa
Atom Count: 62,232
Modeled Residue Count: 7,752
Deposited Residue Count: 20,304
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate synthase	A B [auth C] C [auth E] D [auth G] E [auth I] A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K], G [auth M], H [auth O], I [auth Q], J [auth S], K [auth V], L [auth X], M [auth Z], N [auth BA], O [auth DA], P [auth FA], Q [auth HA], R [auth JA], S [auth LA], T [auth NA], U [auth PA], V [auth RA], W [auth TA], X [auth VA]	846	Staphylothermus marinus F1	Mutation(s): 0 Gene Names: ppsA, Smar_0141 EC: 2.7.9.2
UniProt
Find proteins for P46893 (Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1)) Explore P46893 Go to UniProtKB: P46893
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P46893
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth A] SDF format, chain VA SDF format, chain UA [auth TA] SDF format, chain TA [auth RA] SDF format, chain SA [auth PA] SDF format, chain RA [auth NA] SDF format, chain QA [auth LA] SDF format, chain PA [auth JA] SDF format, chain OA [auth HA] SDF format, chain NA [auth FA] SDF format, chain MA [auth DA] SDF format, chain LA [auth BA] SDF format, chain KA [auth Z] SDF format, chain JA [auth X] SDF format, chain IA [auth V] SDF format, chain HA [auth S] SDF format, chain GA [auth Q] SDF format, chain FA [auth O] SDF format, chain EA [auth M] SDF format, chain DA [auth K] SDF format, chain CA [auth I] SDF format, chain BA [auth G] SDF format, chain AA [auth E] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain VA MOL2 format, chain UA [auth TA] MOL2 format, chain TA [auth RA] MOL2 format, chain SA [auth PA] MOL2 format, chain RA [auth NA] MOL2 format, chain QA [auth LA] MOL2 format, chain PA [auth JA] MOL2 format, chain OA [auth HA] MOL2 format, chain NA [auth FA] MOL2 format, chain MA [auth DA] MOL2 format, chain LA [auth BA] MOL2 format, chain KA [auth Z] MOL2 format, chain JA [auth X] MOL2 format, chain IA [auth V] MOL2 format, chain HA [auth S] MOL2 format, chain GA [auth Q] MOL2 format, chain FA [auth O] MOL2 format, chain EA [auth M] MOL2 format, chain DA [auth K] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain VA mmCIF format, chain UA [auth TA] mmCIF format, chain TA [auth RA] mmCIF format, chain SA [auth PA] mmCIF format, chain RA [auth NA] mmCIF format, chain QA [auth LA] mmCIF format, chain PA [auth JA] mmCIF format, chain OA [auth HA] mmCIF format, chain NA [auth FA] mmCIF format, chain MA [auth DA] mmCIF format, chain LA [auth BA] mmCIF format, chain KA [auth Z] mmCIF format, chain JA [auth X] mmCIF format, chain IA [auth V] mmCIF format, chain HA [auth S] mmCIF format, chain GA [auth Q] mmCIF format, chain FA [auth O] mmCIF format, chain EA [auth M] mmCIF format, chain DA [auth K] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth G] CA [auth I] DA [auth K] EA [auth M] AA [auth E], BA [auth G], CA [auth I], DA [auth K], EA [auth M], FA [auth O], GA [auth Q], HA [auth S], IA [auth V], JA [auth X], KA [auth Z], LA [auth BA], MA [auth DA], NA [auth FA], OA [auth HA], PA [auth JA], QA [auth LA], RA [auth NA], SA [auth PA], TA [auth RA], UA [auth TA], VA, Y [auth A], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth G] Focus chain CA [auth I] Focus chain DA [auth K] Focus chain EA [auth M] Focus chain FA [auth O] Focus chain GA [auth Q] Focus chain HA [auth S] Focus chain IA [auth V] Focus chain JA [auth X] Focus chain KA [auth Z] Focus chain LA [auth BA] Focus chain MA [auth DA] Focus chain NA [auth FA] Focus chain OA [auth HA] Focus chain PA [auth JA] Focus chain QA [auth LA] Focus chain RA [auth NA] Focus chain SA [auth PA] Focus chain TA [auth RA] Focus chain UA [auth TA] Focus chain VA Focus chain Y [auth A] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth G] Focus chain CA [auth I] Focus chain DA [auth K] Focus chain EA [auth M] Focus chain FA [auth O] Focus chain GA [auth Q] Focus chain HA [auth S] Focus chain IA [auth V] Focus chain JA [auth X] Focus chain KA [auth Z] Focus chain LA [auth BA] Focus chain MA [auth DA] Focus chain NA [auth FA] Focus chain OA [auth HA] Focus chain PA [auth JA] Focus chain QA [auth LA] Focus chain RA [auth NA] Focus chain SA [auth PA] Focus chain TA [auth RA] Focus chain UA [auth TA] Focus chain VA Focus chain Y [auth A] Focus chain Z [auth C]