6AFP | pdb_00006afp

Crystal structure of class A b-lactamase, PenL, variant Asn136Asp, from Burkholderia thailandensis, in complex with ceftazidime-like boronic acid

• PDB DOI: https://doi.org/10.2210/pdb6AFP/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia thailandensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-08-08 Released: 2020-01-15 
• Deposition Author(s): Cao, T.-P., Choi, J.M., Lee, S.H.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.175 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Non-catalytic-Region Mutations Conferring Transition of Class A beta-Lactamases Into ESBLs.

Cao, T.-P., Yi, H., Dhanasingh, I., Ghosh, S., Choi, J.M., Lee, K.H., Ryu, S., Kim, H.S., Lee, S.H.

(2020) Front Mol Biosci 

• DOI: https://doi.org/10.3389/fmolb.2020.598998

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.08 kDa 
• Atom Count: 4,852 
• Modeled Residue Count: 536 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	268	Burkholderia thailandensis	Mutation(s): 1  Gene Names: A8H35_31635 EC: 3.5.2.6
UniProt
Find proteins for Q2T5A3 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T5A3  Go to UniProtKB:  Q2T5A3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CB4 (Subject of Investigation/LOI)	C [auth A], E [auth B]	PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE C10 H15 B N4 O6 S ZECCQELUYUPTSB-UUASQNMZSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.175 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.883	α = 90
b = 92.393	β = 94.27
c = 68.841	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Cao, T.-P., Choi, J.M., Lee, S.H.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2016R1D1A1B03932717

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2020-12-09
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description