8GPW | pdb_00008gpw

Structure of Penicillin-binding protein 3 (PBP3) from Klebsiella pneumoniae with ligand 18G

• PDB DOI: https://doi.org/10.2210/pdb8GPW/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-27 Released: 2022-11-02 
• Deposition Author(s): Song, D.Q., Li, Y.H.
• Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.236 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structure of Penicillin-binding protein 3 (PBP3) from Klebsiella pneumoniae with ligand 18G at 2.06 Angstroms resolution

Song, D.Q., Li, Y.H.

To be published.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.18 kDa 
• Atom Count: 6,208 
• Modeled Residue Count: 794 
• Deposited Residue Count: 820 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A, B	410	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: ftsI, ETE64_07005 EC: 3.4.16.4
UniProt
Find proteins for A0A0H3GN85 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GN85  Go to UniProtKB:  A0A0H3GN85

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JXJ (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-[(~{Z})-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2~{S})-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxycyclopropane-1-carboxylic acid C14 H19 N5 O9 S2 IGCRMLSJLQPZRL-ZWJKEBRUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.236 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.4	α = 90
b = 103.66	β = 90
c = 80.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Song, D.Q., Li, Y.H.

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Funding Organization	Location	Grant Number
CAMS Innovation Fund for Medical Sciences (CIFMS)	United Kingdom	2021-I2M-1-070
CAMS Innovation Fund for Medical Sciences (CIFMS)	United Kingdom	2021-I2M-1-030

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary