6AFO | pdb_00006afo

Crystal structure of class A b-lactamase, PenL, variant Asn136Asp, from Burkholderia thailandensis

PDB DOI: https://doi.org/10.2210/pdb6AFO/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.174 (Depositor), 0.174 (DCC)
R-Value Work:
0.147 (Depositor), 0.151 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6AFO

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 57.36 kDa
Atom Count: 4,876
Modeled Residue Count: 536
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2T5A3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.174 (Depositor), 0.174 (DCC)
R-Value Work: 0.147 (Depositor), 0.151 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.986	α = 90
b = 92.723	β = 92.72
c = 68.878	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.