6U2Z

Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed moxalactam and two copper ions

• PDB DOI: https://doi.org/10.2210/pdb6U2Z/pdb

• Classification: HYDROLASE
• Organism(s): Stenotrophomonas maltophilia K279a
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-21 Released: 2019-09-04 
• Deposition Author(s): Kim, Y., Maltseva, N., 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: 2.38 Å
• R-Value Free: 0.229 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed moxalactam and two copper ions

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.77 kDa 
• Atom Count: 2,102 
• Modelled Residue Count: 266 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)	A	274	Stenotrophomonas maltophilia K279a	Mutation(s): 0  Gene Names: Smlt2667 EC: 3.5.2.6
UniProt
Find proteins for B2FTM1 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FTM1  Go to UniProtKB:  B2FTM1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3P7 (Subject of Investigation/LOI)	B [auth A]	(2R)-2-[(1R)-1-{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3 -oxazine-4-carboxylic acid C18 H18 N2 O9 GOYCBKVVHGALFQ-PJSAGSTRSA-N
CU	C [auth A], D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.229 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.234	α = 90
b = 104.234	β = 90
c = 98.793	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Kim, Y., Maltseva, N., 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: 2019-09-04
  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, Structure summary
• Version 1.3: 2023-11-29
  Changes: Database references