3HTI | pdb_00003hti

Crystal structure of multidrug binding protein EbrR complexed with malachite green

PDB DOI: https://doi.org/10.2210/pdb3HTI/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: 2.50 Å
R-Value Free:
0.286 (Depositor), 0.262 (DCC)
R-Value Work:
0.254 (Depositor), 0.266 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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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: 23.6 kDa
Atom Count: 1,356
Modeled Residue Count: 173
Deposited Residue Count: 217
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EbrA repressor	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGR Query on MGR Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MALACHITE GREEN C₂₃ H₂₅ N₂ VFCNQNZNPKRXIT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.286 (Depositor), 0.262 (DCC)
R-Value Work: 0.254 (Depositor), 0.266 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.91	α = 90
b = 59.91	β = 90
c = 110.236	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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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

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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.