3L4E

1.5A Crystal Structure of a Putative Peptidase E Protein from Listeria monocytogenes EGD-e

PDB DOI: https://doi.org/10.2210/pdb3L4E/pdb

Classification: HYDROLASE
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-12-19 Released: 2010-07-14
Deposition Author(s): Brunzelle, J.S., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.222
R-Value Work: 0.169
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

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

Literature

1.5A Crystal Structure of a Putative Peptidase E Protein from Listeria monocytogenes EGD-e

Brunzelle, J.S., Onopriyenko, O., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 23.16 kDa
Atom Count: 1,844
Modelled Residue Count: 202
Deposited Residue Count: 206
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized peptidase Lmo0363	A	206	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: lmo0363 EC: 3.4.21
UniProt
Find proteins for P58495 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P58495 Go to UniProtKB: P58495
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P58495
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 B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.222
R-Value Work: 0.169
R-Value Observed: 0.169
Space Group: P 6₅ 2 2
Diffraction Data: https://doi.org/10.18430/m33l4e

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.821	α = 90
b = 67.821	β = 90
c = 155.169	γ = 120

Software Package:

Software Name	Purpose
BLU-MAX	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Brunzelle, J.S.

Onopriyenko, O.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

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.