7VX3 | pdb_00007vx3

OXA-58 crystal structure of acylated meropenem complex 2

• PDB DOI: https://doi.org/10.2210/pdb7VX3/pdb

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


• Deposited: 2021-11-12 Released: 2022-11-23 
• Deposition Author(s): Saino, H., Sugiyabu, T., Miyano, M.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.163 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

OXA-58 crystal structure of acylated meropenem complex 2

Saino, H., Sugiyabu, T., Miyano, M.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.37 kDa 
• Atom Count: 2,185 
• Modeled Residue Count: 237 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	280	Acinetobacter baumannii	Mutation(s): 0  Gene Names: blaOXA-58, bla-oxa-58, bla-oxa58 EC: 3.5.2.6
UniProt
Find proteins for Q2TR58 (Acinetobacter baumannii) Explore Q2TR58  Go to UniProtKB:  Q2TR58

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DWZ (Subject of Investigation/LOI)	D [auth A]	(2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C17 H27 N3 O5 S UUIYVKJXUXGPKB-VGWSNGFZSA-N
MER (Subject of Investigation/LOI)	C [auth A]	(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid C17 H27 N3 O5 S DYQHXZPAIVAJRU-HTXLXMOSSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.163 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.29	α = 90
b = 75.29	β = 90
c = 119.47	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
MOLREP	phasing
CrystalClear	data collection
iMOSFLM	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Saino, H., Sugiyabu, T., Miyano, M.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	S1311005
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18K07118

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description