5V5T | pdb_00005v5t

Crystal structure of leucine-rich protein regulator, ElrR, from Enterococcus faecalis

PDB DOI: https://doi.org/10.2210/pdb5V5T/pdb

Classification: TRANSCRIPTION
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-15 Released: 2018-09-19
Deposition Author(s): De Groote, M.C.R., Camargo, I.L., Serror, P., Horjales, E.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP), USP/COFECUB International agreement

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.242 (Depositor), 0.214 (DCC)
R-Value Work:
0.196 (Depositor), 0.213 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5V5T

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure and functional characterization of ElrR, a member of the RRNPP family of transcriptional regulators.

De Groote, M.C.R., Camargo, I.L., Repoila, F., Horjales, E., Serror, P.

To be published.

Macromolecule Content

Total Structure Weight: 144.98 kDa
Atom Count: 10,218
Modeled Residue Count: 1,213
Deposited Residue Count: 1,224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved domain protein	A, B, C, D	306	Enterococcus faecalis V583	Mutation(s): 0 Gene Names: EF_2687
UniProt
Find proteins for Q830T5 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830T5 Go to UniProtKB: Q830T5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q830T5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.242 (Depositor), 0.214 (DCC)
R-Value Work: 0.196 (Depositor), 0.213 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.8	α = 112.99
b = 75.33	β = 89.93
c = 85.28	γ = 103.88

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	model building
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-09-19

Deposition Author(s):

De Groote, M.C.R.

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2013/26313-5
USP/COFECUB International agreement	France	2012-22

Revision History (Full details and data files)

Version 1.0: 2018-09-19
Type: Initial release
Version 1.1: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Refinement description, Structure summary

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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.