8F67 | pdb_00008f67

Crystal structure of the refolded Penicillin Binding Protein 5 (PBP5) of Enterococcus faecium

PDB DOI: https://doi.org/10.2210/pdb8F67/pdb

Classification: ANTIBIOTIC
Organism(s): Enterococcus faecium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-11-16 Released: 2023-07-05
Deposition Author(s): D'Andrea, E.D., Schoenle, M.V., Choy, M.S., Peti, W., Page, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.59 Å
R-Value Free:
0.214 (Depositor), 0.210 (DCC)
R-Value Work:
0.180 (Depositor), 0.179 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8F67

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

Literature

The Molecular Basis for Resistance of E. faecium PBP5 to beta-lactam Antibiotics

Hunashal, Y., Kumar, G.S., Choy, M.S., Da Silva Santiago, A., D'Andrea, E.D., Schoenle, M.V., Arthur, M., Rice, L.B., Page, R., Peti, W.

(2023) Nat Commun

Macromolecule Content

Total Structure Weight: 215.92 kDa
Atom Count: 14,680
Modeled Residue Count: 1,920
Deposited Residue Count: 1,929
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pbp5	A, B, C	643	Enterococcus faecium	Mutation(s): 0 Gene Names: pbp5
UniProt
Find proteins for A0A075Q0W3 (Enterococcus faecium) Explore A0A075Q0W3 Go to UniProtKB: A0A075Q0W3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A075Q0W3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DB [auth C] SDF format, chain HA [auth B] SDF format, chain JB [auth C] SDF format, chain U [auth A] SDF format, chain Y [auth B] SDF format, chain ZA [auth C] SDF format, chain Z [auth B] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain X [auth A] SDF format, chain WA [auth C] SDF format, chain W [auth A] SDF format, chain VA [auth C] SDF format, chain V [auth A] SDF format, chain UA [auth C] SDF format, chain TA [auth B] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain QB [auth C] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PB [auth C] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OB [auth C] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NB [auth C] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MB [auth C] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LB [auth C] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KB [auth C] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IB [auth C] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HB [auth C] SDF format, chain H [auth A] SDF format, chain GB [auth C] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FB [auth C] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EB [auth C] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain D [auth A] SDF format, chain CB [auth C] SDF format, chain CA [auth B] SDF format, chain BB [auth C] SDF format, chain BA [auth B] SDF format, chain AB [auth C] SDF format, chain AA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain U [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QB [auth C] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PB [auth C] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OB [auth C] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KB [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain JB [auth C] mmCIF format, chain U [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QB [auth C] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PB [auth C] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OB [auth C] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth C] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth C] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KB [auth C] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth C] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], D [auth A], DA [auth B], DB [auth C], E [auth A], EA [auth B], EB [auth C], F [auth A], FA [auth B], FB [auth C], G [auth A], GA [auth B], GB [auth C], H [auth A], HA [auth B], HB [auth C], I [auth A], IA [auth B], IB [auth C], J [auth A], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], L [auth A], LA [auth B], LB [auth C], M [auth A], MA [auth B], MB [auth C], N [auth A], NA [auth B], NB [auth C], O [auth A], OA [auth B], OB [auth C], P [auth A], PA [auth B], PB [auth C], Q [auth A], QA [auth B], QB [auth C], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain D [auth A] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain D [auth A] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain E [auth A] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth C] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth C] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.59 Å
R-Value Free: 0.214 (Depositor), 0.210 (DCC)
R-Value Work: 0.180 (Depositor), 0.179 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.937	α = 90
b = 331.666	β = 90
c = 156.179	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, 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.