7VVI | pdb_00007vvi

OXA-58 crystal structure of acylated meropenem complex

• PDB DOI: https://doi.org/10.2210/pdb7VVI/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-11-06 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: 1.40 Å
• R-Value Free: 
  0.149 (Depositor), 0.146 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.141 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

OXA-58 crystal structure of acylated meropenem complex

Saino, H., Okimoto, N., Otsuka, T., Sugiyabu, T., Sasaki, I., Ueno, G., Oouchi, M., Yamamoto, M., Ishii, K., Taiji, M., Miyano, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.26 kDa 
• Atom Count: 2,309 
• Modeled Residue Count: 237 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	252	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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: 1.40 Å
• R-Value Free:  0.149 (Depositor), 0.146 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.141 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.38	α = 90
b = 75.38	β = 90
c = 119.531	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building

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