9C3D

Crystal structure of metallo-beta-lactamase superfamily protein CcrA-like_MBL-B1 from Dyadobacter fermentans

• PDB DOI: https://doi.org/10.2210/pdb9C3D/pdb

• Classification: HYDROLASE
• Organism(s): Dyadobacter fermentans DSM 18053
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-31 Released: 2024-07-17 
• Deposition Author(s): Kim, Y., Maltseva, N., Welk, L., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
• 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: 1.85 Å
• R-Value Free: 0.211 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Starting Model: in silico

Literature

Crystal structure of metallo-beta-lactamase superfamily protein CcrA-like_MBL-B1 from Dyadobacter fermentans

Kim, Y., Maltseva, N., Welk, L., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)

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: 25.02 kDa 
• Atom Count: 1,898 
• Modelled Residue Count: 224 
• Deposited Residue Count: 225 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A	225	Dyadobacter fermentans DSM 18053	Mutation(s): 0  Gene Names: Dfer_1371 EC: 3.5.2.6
UniProt
Find proteins for C6W709 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6W709  Go to UniProtKB:  C6W709

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.211 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.176	α = 90
b = 62.256	β = 90
c = 72.387	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Kim, Y., Maltseva, N., Welk, L., Endres, M., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)

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

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release