2GBY | pdb_00002gby

Structure of QacR Multidrug Transcriptional Regulator Bound to Bivalent Diamidine Berenil

PDB DOI: https://doi.org/10.2210/pdb2GBY/pdb

Classification: TRANSCRIPTION
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-03-12 Released: 2008-04-08
Deposition Author(s): Schuman, J.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.290 (Depositor), 0.280 (DCC)
R-Value Work:
0.249 (Depositor), 0.240 (DCC)
R-Value Observed:
0.249 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure of QacR Multidrug Transcriptional Regulator Bound to Trivalent and Bivalent Diamidine Drugs

Brennan, R.G., Schuman, J.T.

To be published.

Macromolecule Content

Total Structure Weight: 93.27 kDa
Atom Count: 6,272
Modeled Residue Count: 744
Deposited Residue Count: 776
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator qacR	A [auth B], B [auth D], C [auth A], D [auth E]	194	Staphylococcus aureus	Mutation(s): 2 Gene Names: qacR
UniProt
Find proteins for P0A0N4 (Staphylococcus aureus) Explore P0A0N4 Go to UniProtKB: P0A0N4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A0N4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BRN Query on BRN Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	BERENIL C₁₄ H₁₅ N₇ XNYZHCFCZNMTFY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain F [auth D] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth E] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth D] MOL2 format, chain F [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth E] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth D] mmCIF format, chain F [auth D] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth E] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	E [auth D] F [auth D] H [auth A] I [auth A] J [auth A] E [auth D], F [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth E], O [auth E], P [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth D] Focus chain F [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain E [auth D] Focus chain F [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.290 (Depositor), 0.280 (DCC)
R-Value Work: 0.249 (Depositor), 0.240 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.34	α = 90
b = 171.34	β = 90
c = 94.53	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-04-08

Deposition Author(s):

Schuman, J.T.

Revision History (Full details and data files)

Version 1.0: 2008-04-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2024-02-14
Changes: Data collection

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Structure of QacR Multidrug Transcriptional Regulator Bound to Bivalent Diamidine Berenil

Structure of QacR Multidrug Transcriptional Regulator Bound to Trivalent and Bivalent Diamidine Drugs

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations