3HTH | pdb_00003hth

Crystal structure of multidrug binding protein EbrR complexed with proflavin

PDB DOI: https://doi.org/10.2210/pdb3HTH/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Streptomyces lividans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-11 Released: 2010-07-14
Deposition Author(s): Dong, J., Ni, L., Schumacher, M., Brennan, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.277 (Depositor), 0.243 (DCC)
R-Value Work:
0.228 (Depositor), 0.239 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural plasticity is key to multiple ligand binding by the multidrug binding regulator EbrR

Dong, J., Ni, L., Schumacher, M., Brennan, R.

To be published.

Macromolecule Content

Total Structure Weight: 70.39 kDa
Atom Count: 4,012
Modeled Residue Count: 514
Deposited Residue Count: 651
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EbrA repressor	A, B, C	217	Streptomyces lividans	Mutation(s): 0 Gene Names: ebrR
UniProt
Find proteins for Q79SH7 (Streptomyces lividans) Explore Q79SH7 Go to UniProtKB: Q79SH7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79SH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRL Query on PRL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B]	PROFLAVIN C₁₃ H₁₁ N₃ WDVSHHCDHLJJJR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth C] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], H [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.277 (Depositor), 0.243 (DCC)
R-Value Work: 0.228 (Depositor), 0.239 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.719	α = 90
b = 99.719	β = 90
c = 133.73	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

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
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

3HTH | pdb_00003hth

Crystal structure of multidrug binding protein EbrR complexed with proflavin

Literature

Structural plasticity is key to multiple ligand binding by the multidrug binding regulator EbrR

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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