9WP7 | pdb_00009wp7

Crystal structure of phosphate binding protein(SphX) from Synechocystis sp. PCC 6803

PDB DOI: https://doi.org/10.2210/pdb9WP7/pdb

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

Deposited: 2025-09-08 Released: 2026-09-16
Deposition Author(s): Wang, C.Y., Lu, Y.P., Ma, H.L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.195 (Depositor), 0.194 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of phosphate binding protein(SphX) from Synechocystis sp. PCC 6803

Wang, C.Y., Lu, Y.P., Ma, H.L.

To be published.

Macromolecule Content

Total Structure Weight: 70.32 kDa
Atom Count: 5,356
Modeled Residue Count: 607
Deposited Residue Count: 624
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SphX	A	311	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Gene Names: sphX, sll0679
UniProt
Find proteins for Q55200 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55200 Go to UniProtKB: Q55200
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55200
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SphX	B	313	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Gene Names: sphX, sll0679
UniProt
Find proteins for Q55200 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55200 Go to UniProtKB: Q55200
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55200
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain I [auth A]	C [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B]	L [auth A], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain R [auth B] Interactions & Density Focus chain L [auth A] Focus chain R [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B]	K [auth A], Q [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain Q [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]