8YM3 | pdb_00008ym3

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

• PDB DOI: https://doi.org/10.2210/pdb8YM3/pdb

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


• Deposited: 2024-03-08 Released: 2025-03-19 
• Deposition Author(s): Cheng, C., Ma, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

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

Chen, C., Ma, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.92 kDa 
• Atom Count: 3,603 
• Modelled Residue Count: 408 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

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
UniProt
Find proteins for P18668 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)) Explore P18668  Go to UniProtKB:  P18668

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL (Subject of Investigation/LOI)	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME (Subject of Investigation/LOI)	E [auth A], F [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.897	α = 90
b = 86.548	β = 95.74
c = 60.775	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Cheng, C., Ma, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271358

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release