9LOW | pdb_00009low

Crystal structure of RamR3.0 complexed with 3-alkenynaphthoate

PDB DOI: https://doi.org/10.2210/pdb9LOW/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-01-23 Released: 2025-10-22
Deposition Author(s): Chen, X., Qian, J.Y., Yang, X.J., Wu, Y.Z., Zhong, F.R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.287 (Depositor), 0.291 (DCC)
R-Value Work:
0.250 (Depositor), 0.252 (DCC)
R-Value Observed:
0.252 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Enantioselective energy transfer catalysis compartmentalized by triplet photoenzymes

Yang, X.J., Guo, J., Qian, J.Y., Huang, J., Shi, J., Jiang, M., Zhang, J., Pang, T., Sun, N., Fu, Y., Zhao, W., Wu, G., Chen, X., Wu, Y.Z., Zhong, F.R.

(2025) Nat Catal

DOI: https://doi.org/10.1038/s41929-025-01433-3

Macromolecule Content

Total Structure Weight: 95.03 kDa
Atom Count: 6,062
Modeled Residue Count: 732
Deposited Residue Count: 812
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative regulatory protein	A, B, C, D	203	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	Mutation(s): 4 Gene Names: STM14_0676
UniProt
Find proteins for A0A0F6AY66 (Salmonella typhimurium (strain 14028s / SGSC 2262)) Explore A0A0F6AY66 Go to UniProtKB: A0A0F6AY66
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0F6AY66
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EKZ (Subject of Investigation/LOI) Query on A1EKZ Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth C], M [auth D]	(phenylmethyl) 1-but-3-enoxynaphthalene-2-carboxylate C₂₂ H₂₀ O₃ AUJGTGJXUCGBFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain M [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	F [auth A] I [auth C] J [auth C] K [auth C] L [auth C] F [auth A], I [auth C], J [auth C], K [auth C], L [auth C], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D]