7ME2 | pdb_00007me2

YfeA oligomer crystal 2, form 2

PDB DOI: https://doi.org/10.2210/pdb7ME2/pdb

Classification: METAL TRANSPORT
Organism(s): Yersinia pestis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-04-06 Released: 2021-08-25
Deposition Author(s): Radka, C.D., Aller, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.184 (Depositor), 0.211 (DCC)
R-Value Work:
0.152 (Depositor)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Site 2 of the Yersinia pestis substrate-binding protein YfeA is a dynamic surface metal-binding site

Radka, C.D., Aller, S.G.

(2021) Acta Crystallogr F Struct Biol Commun 77: 286-293

DOI: https://doi.org/10.1107/S2053230X21008086

Macromolecule Content

Total Structure Weight: 72.79 kDa
Atom Count: 4,974
Modeled Residue Count: 554
Deposited Residue Count: 646
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic chelated iron-binding protein YfeA	A, B	323	Yersinia pestis	Mutation(s): 0 Gene Names: yfeA, YPO2439, y1897, YP_2227
UniProt
Find proteins for Q56952 (Yersinia pestis) Explore Q56952 Go to UniProtKB: Q56952
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q56952
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth B]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], M [auth B], N [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth B] Focus chain N [auth B]