7TRV

Crystal Structure of the DNA-Binding Domain of the LysR family Transcriptional Regulator YfbA from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb7TRV/pdb

Classification: TRANSCRIPTION
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-01-31 Released: 2022-02-09
Deposition Author(s): Kim, Y., Tesar, C., Crawford, M., Chhor, G., Endres, M., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.232
R-Value Work: 0.187
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of the DNA-Binding Domain of the LysR family Transcriptional Regulator YfbA from Yersinia pestis

Kim, Y., Tesar, C., Crawford, M., Chhor, G., Endres, M., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 42.74 kDa
Atom Count: 3,133
Modelled Residue Count: 353
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysR-family transcriptional regulatory protein	A, B, C, D	90	Yersinia pestis CO92	Mutation(s): 0 Gene Names: lysR10, y2171, YP_1951
UniProt
Find proteins for A0A380PDL3 (Yersinia pestis) Explore A0A380PDL3 Go to UniProtKB: A0A380PDL3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A380PDL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth D]	E [auth A] H [auth A] I [auth A] N [auth B] Q [auth C] E [auth A], H [auth A], I [auth A], N [auth B], Q [auth C], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain X [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D]	J [auth B], P [auth C], R [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain P [auth C] Focus chain R [auth D] Interactions & Density Focus chain J [auth B] Focus chain P [auth C] Focus chain R [auth D]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain M [auth B] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	M [auth B], V [auth D], W [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain M [auth B] Focus chain V [auth D] Focus chain W [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	F [auth A] G [auth A] K [auth B] L [auth B] O [auth C] F [auth A], G [auth A], K [auth B], L [auth B], O [auth C], S [auth D], T [auth D], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]