4EF1 | pdb_00004ef1

Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb4EF1/pdb

Classification: METHIONINE-BINDING PROTEIN
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-03-28 Released: 2012-04-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.188 (Depositor), 0.200 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a pheromone cOB1 precursor/lipoprotein, YaeC family (EF2496) from Enterococcus faecalis V583 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 55.33 kDa
Atom Count: 4,469
Modeled Residue Count: 490
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pheromone cOB1/lipoprotein, YaeC family	A, B	246	Enterococcus faecalis V583	Mutation(s): 0 Gene Names: EF_2496
UniProt
Find proteins for Q831K8 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q831K8 Go to UniProtKB: Q831K8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q831K8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MSE Query on MSE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SELENOMETHIONINE C₅ H₁₁ N O₂ Se RJFAYQIBOAGBLC-BYPYZUCNSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.188 (Depositor), 0.200 (DCC)
R-Value Observed: 0.191 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34EF1

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.923	α = 90
b = 96.485	β = 100.55
c = 69.042	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-04-25
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: 2024-10-30
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.