8YLY | pdb_00008yly

Structural basis of Elongation factor Tu in regulating photoinhibition in Synechococcus sp. PCC 7942.

PDB DOI: https://doi.org/10.2210/pdb8YLY/pdb

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

Deposited: 2024-03-07 Released: 2025-03-19
Deposition Author(s): Cheng, C., Ma, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.193 (Depositor), 0.192 (DCC)
R-Value Work:
0.176 (Depositor), 0.177 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis of Elongation factor Tu in regulating photoinhibition in Synechococcus sp. PCC 7942

Chen, C., Ma, H.

To be published.

Macromolecule Content

Total Structure Weight: 45.45 kDa
Atom Count: 3,646
Modeled Residue Count: 404
Deposited Residue Count: 408
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Tu	A	408	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0 Gene Names: tuf, tufA, syc0656_d EC: 3.6.5.3
UniProt
Find proteins for P33171 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore P33171 Go to UniProtKB: P33171
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33171
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	B [auth A] F [auth A] G [auth A] H [auth A] K [auth A] B [auth A], F [auth A], G [auth A], H [auth A], K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain B [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain L [auth A]
BME (Subject of Investigation/LOI) Query on BME Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	C [auth A], E [auth A], I [auth A], J [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain I [auth A] Focus chain J [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]