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

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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

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

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55410
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55410
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55410
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55410
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain I [auth B]	G [auth A], I [auth B], K [auth C], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain H [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain H [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain H [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth A], J [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth C]