6T5K

ECV-1 from Echinicola vietnamensis. Environmental metallo-beta-lactamases exhibit high enzymatic activity under zinc deprivation

• PDB DOI: https://doi.org/10.2210/pdb6T5K/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Echinicola vietnamensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-16 Released: 2020-05-27 
• Deposition Author(s): Frohlich, C.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.183 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 

Literature

Structural and biochemical characterization of the environmental MBLs MYO-1, ECV-1 and SHD-1.

Frohlich, C., Sorum, V., Huber, S., Samuelsen, O., Berglund, F., Kristiansson, E., Kotsakis, S.D., Marathe, N.P., Larsson, D.G.J., Leiros, H.S.

(2020) J Antimicrob Chemother 75: 2554-2563

• PubMed: 32464640 
• DOI: https://doi.org/10.1093/jac/dkaa175
• Primary Citation of Related Structures:  
  6T5K, 6T5L


• PubMed Abstract: 
  

  MBLs form a large and heterogeneous group of bacterial enzymes conferring resistance to β-lactam antibiotics, including carbapenems. A large environmental reservoir of MBLs has been identified, which can act as a source for transfer into human pathogens. Therefore, structural investigation of environmental and clinically rare MBLs can give new insights into structure-activity relationships to explore the role of catalytic and second shell residues, which are under selective pressure.

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Organizational Affiliation: 

The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.83 kDa 
• Atom Count: 2,108 
• Modelled Residue Count: 224 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zn-dependent hydrolase, glyoxylase	A [auth C]	240	Echinicola vietnamensis	Mutation(s): 0  Gene Names: Echvi_2632
UniProt
Find proteins for L0FY79 (Echinicola vietnamensis (strain DSM 17526 / LMG 23754 / KMM 6221)) Explore L0FY79  Go to UniProtKB:  L0FY79

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	G [auth C], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth C], C, D [auth C], E [auth C], F [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.183 
• R-Value Work: 0.147 
• R-Value Observed: 0.149 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.926	α = 90
b = 65.676	β = 90
c = 128.501	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Frohlich, C.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2013-08633
Swedish Research Council	Sweden	2018-02835

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 1.2: 2020-09-02
  Changes: Database references, Derived calculations
• Version 1.3: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description