9L8J | pdb_00009l8j

Crystal structure of a putative phosphate binding protein from Synechocystis sp. PCC 6803 reveals an evolutionary hotspot

• PDB DOI: https://doi.org/10.2210/pdb9L8J/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-27 Released: 2025-12-31 
• Deposition Author(s): Wang, C.Y., Ma, H.L., Lu, Y.P.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of a putative phosphate binding protein from Synechocystis sp. PCC 6803 reveals an evolutionary hotspot

Wang, C.Y., Ma, H.L., Lu, Y.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 104.17 kDa 
• Atom Count: 8,138 
• Modeled Residue Count: 955 
• Deposited Residue Count: 968 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sll0540 protein	A	242	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: sll0540
UniProt
Find proteins for Q55410 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55410  Go to UniProtKB:  Q55410

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sll0540 protein	B	242	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: sll0540
UniProt
Find proteins for Q55410 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55410  Go to UniProtKB:  Q55410

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sll0540 protein	C	242	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: sll0540
UniProt
Find proteins for Q55410 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55410  Go to UniProtKB:  Q55410

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Sll0540 protein	D	242	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0  Gene Names: sll0540
UniProt
Find proteins for Q55410 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55410  Go to UniProtKB:  Q55410

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	G [auth A], I [auth B], K [auth C], L [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL (Subject of Investigation/LOI)	E [auth A], F [auth A], H [auth A], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.775	α = 90
b = 117.065	β = 90
c = 120.981	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Wang, C.Y., Ma, H.L., Lu, Y.P.

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Funding Organization	Location	Grant Number
Other government		2024M753349
Other government	China	32271358

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release