4ME8 | pdb_00004me8

Crystal structure of a signal peptidase I (EF3073) from Enterococcus faecalis V583 at 2.27 A resolution

PDB DOI: https://doi.org/10.2210/pdb4ME8/pdb

Classification: HYDROLASE
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-08-25 Released: 2013-09-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.212 (Depositor), 0.220 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a signal peptidase I (EF3073) from Enterococcus faecalis V583 at 2.27 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 17.29 kDa
Atom Count: 958
Modeled Residue Count: 117
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal peptidase I	A	151	Enterococcus faecalis V583	Mutation(s): 0 Gene Names: EF_3073 EC: 3.4.21.89
UniProt
Find proteins for Q82ZI3 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q82ZI3 Go to UniProtKB: Q82ZI3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q82ZI3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density 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: 2.27 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.212 (Depositor), 0.220 (DCC)
R-Value Observed: 0.216 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34ME8

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.488	α = 90
b = 37.488	β = 90
c = 169.046	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-10-16
Changes: Data collection, Structure summary

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.