5CUW | pdb_00005cuw

Crystal structure of Sortase E1 from Streptomyces coelicolor with tripeptide in the active site

PDB DOI: https://doi.org/10.2210/pdb5CUW/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Streptomyces coelicolor A3(2)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-25 Released: 2016-08-17
Deposition Author(s): Kattke, M.D., Cascio, D., Sawaya, M.R., Clubb, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the first class E sortase transpeptidase, SrtE1 from Streptomyces coelicolor

Kattke, M.D., Cascio, D., Sawaya, M.R., Elliot, M.A., Clubb, R.T.

To be published.

Macromolecule Content

Total Structure Weight: 21.34 kDa
Atom Count: 1,267
Modeled Residue Count: 162
Deposited Residue Count: 195
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SrtE1	A	195	Streptomyces coelicolor A3(2)	Mutation(s): 0 Gene Names: SCO3850 EC: 3.4.22.70
UniProt
Find proteins for Q9XA14 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9XA14 Go to UniProtKB: Q9XA14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9XA14
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.227 (Depositor), 0.230 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.11	α = 90
b = 104.3	β = 90
c = 79.02	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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.