6LF4 | pdb_00006lf4

Crystal structure of VMB-1 bound to hydrolyzed meropenem

• PDB DOI: https://doi.org/10.2210/pdb6LF4/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio alginolyticus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-11-28 Released: 2020-03-25 
• Deposition Author(s): Cheng, Q., Chen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of VMB-1 bound to hydrolyzed meropenem

Chen, S., Cheng, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 104.95 kDa 
• Atom Count: 7,156 
• Modeled Residue Count: 876 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VMB-1 metallo-beta-lactamase	A, B, C, D	234	Vibrio alginolyticus	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for A0A5Q5ADH9 (Vibrio alginolyticus) Explore A0A5Q5ADH9  Go to UniProtKB:  A0A5Q5ADH9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMP (Subject of Investigation/LOI)	G [auth A], J [auth B], M [auth C], P [auth D]	(2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoy l)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid C17 H27 N3 O6 S CDYPSIIDXKMBLV-CFINEGTKSA-N
ZN (Subject of Investigation/LOI)	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], N [auth D], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.108	α = 90
b = 96.777	β = 90
c = 131.716	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-25 
Deposition Author(s): Cheng, Q., Chen, S.

Revision History  

• Version 1.0: 2020-03-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary