9QR4 | pdb_00009qr4

InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392

PDB DOI: https://doi.org/10.2210/pdb9QR4/pdb

Classification: CELL INVASION
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-04-03 Released: 2025-12-03
Deposition Author(s): Geerds, C., Niemann, H.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.196 (Depositor), 0.197 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Single mutations to tyrosine or glutamate improve crystallizability and crystal diffraction properties of a flexible two-domain protein

Geerds, C., Niemann, H.H.

(2025) Acta Crystallogr F Struct Biol Commun

Macromolecule Content

Total Structure Weight: 122.46 kDa
Atom Count: 10,160
Modeled Residue Count: 1,072
Deposited Residue Count: 1,086
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Internalin B	A, B, C	362	Listeria monocytogenes EGD-e	Mutation(s): 1 Gene Names: inlB, lmo0434
UniProt
Find proteins for P0DQD2 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P0DQD2 Go to UniProtKB: P0DQD2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DQD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	D [auth A] E [auth A] F [auth A] G [auth B] H [auth B] D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C]