6E0S | pdb_00006e0s

Crystal structure of MEM-A1, a subclass B3 metallo-beta-lactamase isolated from a soil metagenome library

• PDB DOI: https://doi.org/10.2210/pdb6E0S/pdb

• Classification: HYDROLASE
• Organism(s): soil metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-06 Released: 2018-07-25 
• Deposition Author(s): Stogios, P.J., Skarina, T., Lau, C., Topp, E., Savchenko, A., Joachimiak, A., Satchell, K.J., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of MEM-A1, a subclass B3 metallo-beta-lactamase isolated from a soil metagenome library

Stogios, P.J.

To be published.

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: 30.79 kDa 
• Atom Count: 2,433 
• Modeled Residue Count: 264 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEM-A1	A	286	soil metagenome	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.313	α = 90
b = 68.649	β = 90
c = 78.588	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Stogios, P.J., Skarina, T., Lau, C., Topp, E., Savchenko, A., Joachimiak, A., Satchell, K.J., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary