7XG8 | pdb_00007xg8

Crystal structure of PstS protein from cyanophage P-SSM2

PDB DOI: https://doi.org/10.2210/pdb7XG8/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Prochlorococcus phage P-SSM2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-03 Released: 2023-02-08
Deposition Author(s): Cai, K., Jiang, Y.L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.279 (Depositor), 0.282 (DCC)
R-Value Work:
0.227 (Depositor), 0.234 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Biochemical and structural characterization of the cyanophage-encoded phosphate-binding protein: implications for enhanced phosphate uptake of infected cyanobacteria

Zhao, F., Lin, X., Cai, K., Jiang, Y., Ni, T., Chen, Y., Feng, J., Dang, S., Zhou, C.Z., Zeng, Q.

(2022) Environ Microbiol 24: 3037-3050

DOI: https://doi.org/10.1111/1462-2920.16043

Macromolecule Content

Total Structure Weight: 33.91 kDa
Atom Count: 2,248
Modeled Residue Count: 298
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, substrate binding protein, phosphate	A	321	Prochlorococcus phage P-SSM2	Mutation(s): 0 Gene Names: pstS, PCMG_00251, PSSM2_248
UniProt
Find proteins for Q58MA7 (Prochlorococcus phage P-SSM2) Explore Q58MA7 Go to UniProtKB: Q58MA7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58MA7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.279 (Depositor), 0.282 (DCC)
R-Value Work: 0.227 (Depositor), 0.234 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.774	α = 90
b = 63.525	β = 90
c = 108.083	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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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.