9WP4 | pdb_00009wp4

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

PDB DOI: https://doi.org/10.2210/pdb9WP4/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
Expression System: Escherichia coli BL21
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: 1.41 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.176 (Depositor), 0.176 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 71.06 kDa
Atom Count: 5,911
Modeled Residue Count: 659
Deposited Residue Count: 666
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate-binding protein	A	333	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Gene Names: pstS
UniProt
Find proteins for Q55199 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55199 Go to UniProtKB: Q55199
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55199
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate-binding protein	B	333	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Gene Names: pstS
UniProt
Find proteins for Q55199 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore Q55199 Go to UniProtKB: Q55199
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55199
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 C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.236 (Depositor), 0.236 (DCC)
R-Value Work: 0.176 (Depositor), 0.176 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.768	α = 90
b = 64.843	β = 91.39
c = 129.157	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.