6V73 | pdb_00006v73

Crystal Structure of Metallo Beta Lactamase from Erythrobacter litoralis with beta mercaptoethanol in the active site

• PDB DOI: https://doi.org/10.2210/pdb6V73/pdb

• Classification: HYDROLASE
• Organism(s): Erythrobacter litoralis HTCC2594
• Mutation(s): No 


• Deposited: 2019-12-06 Released: 2019-12-25 
• Deposition Author(s): Maltseva, N., Kim, Y., Clancy, S., Endres, M., Mulligan, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.241 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Metallo Beta Lactamase from Erythrobacter litoralis with beta mercaptoethanol in the active site

Maltseva, N., Kim, Y., Clancy, S., Endres, M., Mulligan, R., 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.

Macromolecule Content 

• Total Structure Weight: 26.25 kDa 
• Atom Count: 1,760 
• Modeled Residue Count: 228 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase II	A	245	Erythrobacter litoralis HTCC2594	Mutation(s): 0  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
BME	E [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.241 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.139	α = 90
b = 121.139	β = 90
c = 90.551	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Maltseva, N., Kim, Y., Clancy, S., Endres, M., Mulligan, R., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description