7DDM | pdb_00007ddm

Crystal Structure of PenA39 beta-Lactamase

PDB DOI: https://doi.org/10.2210/pdb7DDM/pdb

Classification: HYDROLASE
Organism(s): Burkholderia multivorans CGD2, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-29 Released: 2021-11-03
Deposition Author(s): Nukaga, M., Hoshino, T., Papp-Wallace, K.M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Veterans Affairs Biomedical Laboratory Research and Development Service, Cystic Fibrosis Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.144 (Depositor), 0.145 (DCC)
R-Value Work:
0.125 (Depositor), 0.128 (DCC)
R-Value Observed:
0.126 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Frameshift mutations in genes encoding PBP3 and PBP4 trigger an unusual, extreme beta-lactam resistance phenotype in Burkholderia multivorans

Nukaga, M., Becka, S.A., Zeiser, E.T., Hoshino, Y., LiPuma, J.J., Papp-Wallace, K.M.

To be published.

Macromolecule Content

Total Structure Weight: 33.44 kDa
Atom Count: 2,347
Modeled Residue Count: 271
Deposited Residue Count: 314
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	302	Burkholderia multivorans CGD2	Mutation(s): 0 Gene Names: BURMUCGD2_4198 EC: 3.5.2.6
UniProt
Find proteins for B9BS30 (Burkholderia multivorans CGD2) Explore B9BS30 Go to UniProtKB: B9BS30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9BS30
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ALA-ARG-ASP-ALA-ALA-VAL-SER-ASP-ALA-ALA-ALA	B [auth E]	12	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.144 (Depositor), 0.145 (DCC)
R-Value Work: 0.125 (Depositor), 0.128 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.519	α = 90
b = 65.519	β = 90
c = 51.421	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Nukaga, M.

Hoshino, T.

Papp-Wallace, K.M.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20K07484
Veterans Affairs Biomedical Laboratory Research and Development Service	United States	BX002872
Cystic Fibrosis Foundation	United States	LIPUMA13I0 and LIPUMA15P0