3DDV | pdb_00003ddv

The crystal structure of the transcriptional regulator (GntR family) from Enterococcus faecalis V583

PDB DOI: https://doi.org/10.2210/pdb3DDV/pdb

Classification: transcription regulator
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-06 Released: 2008-10-07
Deposition Author(s): Zhang, R., Zhou, M., Bargassa, M., Otwinowski, Z., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.251 (Depositor), 0.265 (DCC)
R-Value Work:
0.206 (Depositor), 0.225 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3DDV

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

Literature

The crystal structure of the transcriptional regulator (GntR family) from Enterococcus faecalis V583

Zhang, R., Zhou, M., Bargassa, M., Otwinowski, Z., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 66.46 kDa
Atom Count: 4,252
Modeled Residue Count: 518
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator (GntR family)	A, B, C, D	145	Enterococcus faecalis	Mutation(s): 0 Gene Names: GI:29343357
UniProt
Find proteins for Q835P8 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q835P8 Go to UniProtKB: Q835P8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q835P8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.251 (Depositor), 0.265 (DCC)
R-Value Work: 0.206 (Depositor), 0.225 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.153	α = 90
b = 86.153	β = 90
c = 240.059	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.