5B15 | pdb_00005b15

Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem

• PDB DOI: https://doi.org/10.2210/pdb5B15/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-23 Released: 2016-05-11 
• Deposition Author(s): Wachino, J., Arakawa, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.158 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Doripenem

Wachino, J., Arakawa, Y.

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: 28.77 kDa 
• Atom Count: 2,341 
• Modeled Residue Count: 259 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase	A	262	Serratia marcescens	Mutation(s): 0  Gene Names: SMB-1 EC: 3.5.2.6
UniProt
Find proteins for G5ELM3 (Serratia marcescens) Explore G5ELM3  Go to UniProtKB:  G5ELM3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DQM	N [auth A]	(2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid C15 H26 N4 O7 S2 FODJFDYENOTZNC-UNWFBNKDSA-N
SO4	K [auth A], L [auth A], M [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.158 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.01	α = 107.57
b = 40.92	β = 102.56
c = 45.32	γ = 107.01

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): Wachino, J., Arakawa, Y.

Revision History  

• Version 1.0: 2016-05-11
  Type: Initial release
  
• Version 1.1: 2016-07-06
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary