7RLR | pdb_00007rlr

Crystal Structure of K83A Mutant of Class D beta-lactamase from Clostridium difficile 630

PDB DOI: https://doi.org/10.2210/pdb7RLR/pdb

Classification: HYDROLASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-07-26 Released: 2021-08-11
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Rosas-Lemus, M., Jedrzejczak, R., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.198 (Depositor), 0.200 (DCC)
R-Value Work:
0.168 (Depositor), 0.180 (DCC)
R-Value Observed:
0.170 (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

A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.

Rosas-Lemus, M., Dey, S., Minasov, G., Tan, K., Anderson, S.M., Brunzelle, J., Nocadello, S., Shabalin, I., Filippova, E., Halavaty, A., Kim, Y., Maltseva, N., Osipiuk, J., Minor, W., Joachimiak, A., Savchenko, A., Anderson, W.F., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0050723-e0050723

PubMed: 37747257 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/MRA.00507-23
Primary Citation of Related Structures:
7K1U, 7RL8, 7RLR

PubMed Abstract:
Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.

Organizational Affiliation

Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Macromolecule Content

Total Structure Weight: 117.46 kDa
Atom Count: 9,188
Modeled Residue Count: 1,006
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	255	Clostridioides difficile 630	Mutation(s): 1 Gene Names: CD630_04580 EC: 3.5.2.6
UniProt
Find proteins for Q188Q3 (Clostridioides difficile (strain 630)) Explore Q188Q3 Go to UniProtKB: Q188Q3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q188Q3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	J [auth B], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	G [auth A], I [auth B], M [auth C], R [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain R [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	E [auth A] F [auth A] H [auth B] L [auth C] P [auth D] E [auth A], F [auth A], H [auth B], L [auth C], P [auth D], Q [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	N [auth D], O [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain N [auth D] Focus chain O [auth D]