8U55 | pdb_00008u55

Crystal structure of Enterococcus faecium EnGen25 Penicillin-binding protein 5 (PBP5)

PDB DOI: https://doi.org/10.2210/pdb8U55/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Enterococcus faecium EnGen0025
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-12 Released: 2024-02-07
Deposition Author(s): Pemberton, O.A., Shamoo, Y.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.274 (Depositor), 0.270 (DCC)
R-Value Work:
0.226 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Enterococcus faecium EnGen25 Penicillin-binding protein 5 (PBP5)

Pemberton, O.A., Shamoo, Y.

To be published.

Macromolecule Content

Total Structure Weight: 72.46 kDa
Atom Count: 5,033
Modeled Residue Count: 622
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 5	A	664	Enterococcus faecium EnGen0025	Mutation(s): 0 Gene Names: pbp5
UniProt
Find proteins for M1RM73 (Enterococcus faecium) Explore M1RM73 Go to UniProtKB: M1RM73
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M1RM73
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.274 (Depositor), 0.270 (DCC)
R-Value Work: 0.226 (Depositor), 0.230 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.227	α = 90
b = 62.227	β = 90
c = 372.317	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Pemberton, O.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release

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.