8ZPC | pdb_00008zpc

Acinetobacter baumannii Penicillin-Binding Protein 2

• PDB DOI: https://doi.org/10.2210/pdb8ZPC/pdb

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


• Deposited: 2024-05-29 Released: 2024-12-04 
• Deposition Author(s): Jang, H.S., Park, H.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 
  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: in silico

Literature

Fully closed conformation of penicillin-binding protein revealed by structure of PBP2 from Acinetobacter baumannii.

Jang, H., Kim, C.M., Hong, E., Park, H.H.

(2024) Biochem Biophys Res Commun 729: 150368-150368

• PubMed: 38986258 
• DOI: https://doi.org/10.1016/j.bbrc.2024.150368
• Primary Citation Related Structures: 
  8ZPC


• PubMed Abstract: 
  

  Penicillin-binding protein 2 (PBP2), a vital protein involved in bacterial cell-wall synthesis, serves a target for β-lactam antibiotics. Acinetobacter baumannii is a pathogen notorious for multidrug resistance; therefore, exploration of PBPs is pivotal in the development of new antimicrobial strategies. In this study, the tertiary structure of PBP2 from A. baumannii (abPBP2) was elucidated using X-ray crystallography. The structural analysis demonstrated notable movement in the head domain, potentially critical for its glycosyltransferase function, suggesting that abPBP2 assumes a fully closed conformation. Our findings offer valuable information for developing novel antimicrobial agents targeting abPBP2 that are applicable in combating multidrug-resistant infections.

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Organizational Affiliation: 
• College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.
Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea.
College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 139.32 kDa 
• Atom Count: 8,038 
• Modeled Residue Count: 1,025 
• Deposited Residue Count: 1,262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase MrdA	A, B	631	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  pbpA, ftsI_2, mrdA, A7M90_11050, ABR2091_1008, APD17_02520, AUO97_12320, B9W25_14295, CAS83_05900, CBE85_06915, CV954_014345, EA706_11320, EA722_01945, F4T85_05015, FJU42_01870, G3N53_08595, GSE42_05635, IAG11_14580, IMO23_05010, ITE13_01515, JHZ39_003244, P9867_04120, SAMEA104305318_00781, SAMEA4394745_02684 EC: 3.4.16.4
UniProt
Find proteins for D0C8Z9 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0C8Z9  Go to UniProtKB:  D0C8Z9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.436	α = 90
b = 151.531	β = 90
c = 177.166	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Jang, H.S., Park, H.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release