4E6W | pdb_00004e6w

ClbP in complex with 3-aminophenyl boronic acid

• PDB DOI: https://doi.org/10.2210/pdb4E6W/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli O6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-16 Released: 2013-03-27 
• Deposition Author(s): Cougnoux, A., Delmas, J., Bonnet, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.240 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

The NRP peptidase ClbP as a target for the inhibition of genotoxicity, cell proliferation and tumorogenesis mediated by pks-harboring bacteria

Cougnoux, A., Delmas, J., Dalmasso, G., Romagnoli, C., Cuevas-Ramos, G., Oswald, E., Parti, F., Bonnet, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.38 kDa 
• Atom Count: 8,086 
• Modeled Residue Count: 991 
• Deposited Residue Count: 1,005 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ClbP peptidase	A, B, C	335	Escherichia coli O6	Mutation(s): 0  Gene Names: c2452 EC: 3.5.2.6
UniProt
Find proteins for A0A0H2V8D3 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2V8D3  Go to UniProtKB:  A0A0H2V8D3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
APB	D [auth A], G [auth B], J [auth C]	M-AMINOPHENYLBORONIC ACID C6 H8 B N O2 JMZFEHDNIAQMNB-UHFFFAOYSA-N
PO4	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.240 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.49	α = 90
b = 149.36	β = 124.21
c = 88.24	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Cougnoux, A., Delmas, J., Bonnet, R.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary