6V3U | pdb_00006v3u

Crystal Structure of the NDM_FIM-1 like Metallo-beta-Lactamase from Erythrobacter litoralis in the Mono-Zinc Form

• PDB DOI: https://doi.org/10.2210/pdb6V3U/pdb

• Classification: HYDROLASE
• Organism(s): Erythrobacter litoralis HTCC2594
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-26 Released: 2020-01-15 
• Deposition Author(s): Kim, Y., Maltseva, N., Mulligan, R., Endres, M., Joachimiak, A., 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: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the NDM_FIM-1 like Metallo-beta-Lactamase from Erythrobacter litoralis in the Mono-Zinc Form

Kim, Y., Maltseva, N., Mulligan, R., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 52.76 kDa 
• Atom Count: 3,355 
• Modeled Residue Count: 430 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase II	A, B	242	Erythrobacter litoralis HTCC2594	Mutation(s): 0  Gene Names: ELI_07580 EC: 3.5.2.6
UniProt
Find proteins for Q2N9N3 (Erythrobacter litoralis (strain HTCC2594)) Explore Q2N9N3  Go to UniProtKB:  Q2N9N3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	E [auth A], I [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
OCS	A, B	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.043	α = 90
b = 80.043	β = 90
c = 72.502	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Kim, Y., Maltseva, N., Mulligan, R., Endres, M., Joachimiak, A., 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	--

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description