3d71

Crystal structure of E253Q BMRR bound to 22 base pair promoter site

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Multidrug-efflux transporter 1 regulator

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	BMR promoter DNA × 2 ZINC ION × 2 CITRATE ANION × 2 S-1,2-PROPANEDIOL × 6 TRIFLUOROETHANOL × 2 IMIDAZOLE × 10 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BMRR_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–278； UniProt 1–278

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3d71
Deposition date deposition_date	2008-05-20
Structure title title	Crystal structure of E253Q BMRR bound to 22 base pair promoter site
Keywords keywords	;TRANSCRIPTION REGULATOR, PROTEIN-DNA COMPLEX, MULTIDRUG BINDING PROTEIN, MERR FAMILY, WINGED-HELIX, Activator, DNA-binding, Transcription regulation, TRANSCRIPTION REGULATOR-DNA COMPLEX ;; TRANSCRIPTION REGULATOR/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3d71__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3d71__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d71__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.33 Å
Rg (electron density)	34.34 Å
Total Rg	34.63 Å
Atom count	5626
Residues	600
Excluded volume	97953 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d71__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	BMR promoter DNA
Molecular weight formula_weight	7362.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M
Atom count atom_count	2868

TGACCCTCCCCTTAGGGGAGGGTC

Entity 2 Entity 2 polymer

Description description	Multidrug-efflux transporter 1 regulator
Molecular weight formula_weight	33477.2 kDa
Mutation mutation	E253Q, A277L, E278D
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MKESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYQLIIPIHYSPKKQEEYRVEMKIRILDHHHHHH

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	S-1,2-PROPANEDIOL
Molecular weight formula_weight	76.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	TRIFLUOROETHANOL
Molecular weight formula_weight	100.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	55

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d71a1
Class class	a — All alpha proteins
Fold Fold fold	a.6 — Putative DNA-binding domain
Superfamily Superfamily superfamily	a.6.1 — Putative DNA-binding domain
Family Family family	a.6.1.3 — DNA-binding N-terminal domain of transcription activators

Domain ID domain_id	d3d71a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.1 — Multidrug-binding domain of transcription activator BmrR

CATH v4.4 (3 domains)

Domain ID domain_id	3d71A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1660 — Multidrug-efflux Transporter Regulator; Chain: A; Domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3d71A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	490 — Single helix bin

Domain ID domain_id	3d71A03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

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Unit-cell length a length_a	105.480 Å
Unit-cell length b length_b	105.480 Å
Unit-cell length c length_c	147.330 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	47.170 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2480

Crystal structure of E253Q BMRR bound to 22 base pair promoter site

1. Protein Identity and Related Structures Protein Identity & Related Structures

Multidrug-efflux transporter 1 regulator

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3d71__assembly_1__model_1

3d71__assembly_1__model_1 | I(q)

3d71__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (2)

Crystal structure of E253Q BMRR bound to 22 base pair promoter site

1. Protein Identity and Related Structures Protein Identity & Related Structures

Multidrug-efflux transporter 1 regulator

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3d71__assembly_1__model_1

3d71__assembly_1__model_1 | I(q)

3d71__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (2)