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), 0.272 (DCC)
R-Value Work:
0.226 (Depositor), 0.226 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8U55

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.272 (DCC)
R-Value Work: 0.226 (Depositor), 0.226 (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

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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

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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.