SAXSdb — 3d6y

▼

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

Multidrug-efflux transporter 1 regulator

Bacillus subtilis

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–278	Fragment：residues 1-278 Mutation：R275E, A277L, E278D	BMR promoter DNA × 2 BER BERBERINE × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.0 M Sodium Malonate, 0.05% Jeffamine-M600, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3D6Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BOW MULTIDRUG-BINDING DOMAIN OF TRANSCRIPTION ACTIVATOR BMRR (APO FORM) Deposited 1998-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 121–279（159 aa） Fragment：MULTIDRUG-BINDING DOMAIN	Not recorded	MN MANGANESE (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.70 Å R-free 0.270
1EXI CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTILIS, BOUND TO 21 BASE PAIR BMR OPERATOR AND TPSB Deposited 2000-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	ZN ZINC ION × 2 118 TETRAPHENYLANTIMONIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1 M imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.12 Å R-free 0.317
1EXJ CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTILIS, BOUND TO 21 BASE PAIR BMR OPERATOR AND TPP Deposited 2000-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	NA SODIUM ION × 2 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1 M imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.00 Å R-free 0.315
1R8E Crystal Structure of BmrR Bound to DNA at 2.4A Resolution Deposited 2003-10-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	GOL GLYCEROL × 10 P4P TETRAPHENYLPHOSPHONIUM × 2 IMD IMIDAZOLE × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；Imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.40 Å R-free 0.267
2BOW MULTIDRUG-BINDING DOMAIN OF TRANSCRIPTION ACTIVATOR BMRR IN COMPLEX WITH A LIGAND, TETRAPHENYLPHOSPHONIUM Deposited 1998-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 121–279（159 aa） Fragment：MULTIDRUG-BINDING DOMAIN	Not recorded	MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.80 Å R-free 0.320
2BOW MULTIDRUG-BINDING DOMAIN OF TRANSCRIPTION ACTIVATOR BMRR IN COMPLEX WITH A LIGAND, TETRAPHENYLPHOSPHONIUM Deposited 1998-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 121–279（159 aa） Fragment：MULTIDRUG-BINDING DOMAIN	Not recorded	MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.80 Å R-free 0.320
3D6Z Crystal structure of R275E mutant of BMRR bound to DNA and rhodamine Deposited 2008-05-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa） Fragment：residues 1-278	Mutation：R275E, A277L, E278D	GOL GLYCEROL × 8 RHQ RHODAMINE 6G × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；SODIUM MALONATE, JEFFAMINE-M600, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.263
3D70 Crystal structure of E253A mutant of BMRR bound to 22-bp oligonucleotide Deposited 2008-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	IMD IMIDAZOLE × 12 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；SODIUM CITRATE, IMIDAZOLE, TRIFLUOROETHANOL, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.273
3D71 Crystal structure of E253Q BMRR bound to 22 base pair promoter site Deposited 2008-05-20	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa） Fragment：residues 1-278	Mutation：E253Q, A277L, E278D	ZN ZINC ION × 2 FLC CITRATE ANION × 2 PGO S-1,2-PROPANEDIOL × 6 ETF TRIFLUOROETHANOL × 2 IMD IMIDAZOLE × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；SODIUM CITRATE, IMIDAZOLE, TRIFLUOROETHANOL, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.248
3IAO Conformational plasticity of the coiled coil domain of BmrR is required for bmr promoter binding-the unliganded structure of BmrR Deposited 2009-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–278（278 aa）	Mutation：R275E, E253Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 4000, 0.2 M Lithium Sulfate, 0.1M Tris HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.275
3Q1M Crystal Structure of BmrR Dimer bound to DNA and the ligand 4-amino-quinaldine Deposited 2010-12-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–276（276 aa）	Not recorded	M4A 2-methylquinolin-4-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1.0 M Sodium Malonate, 0.05% Jeffamine-M600, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.20 Å R-free 0.272
3Q2Y Crystal Structure of BmrR bound to ethidium Deposited 2010-12-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	ET ETHIDIUM × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1.0 M Sodium Malonate, 0.05% jeffamine pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.95 Å R-free 0.246
3Q3D Crystal structure of BmrR bound to puromycin Deposited 2010-12-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	PUY PUROMYCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；291 K；1.0 M Sodium Malonate ) 0.05% jeffamine-M600 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.79 Å R-free 0.262
3Q5P Crystal structure of BmrR bound to Tetracycline Deposited 2010-12-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	TAC TETRACYCLINE × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1.0 M Sodium Malonate 0.05% jeffamine pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.94 Å R-free 0.262
3Q5R Crystal structure of BmrR bound to Kanamycin Deposited 2010-12-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	KAN KANAMYCIN A × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1.0 M Sodium Malonate pH 7.0, 0.05% jeffamine M600, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.05 Å R-free 0.247
3Q5S Crystal structure of BmrR bound to Acetylcholine Deposited 2010-12-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–278（278 aa）	Not recorded	ACH ACETYLCHOLINE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；291 K；1.0 M Sodium Malonate ph 7.0 0.05% Jeffamine M600, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.276
7CKQ The cryo-EM structure of B. subtilis BmrR transcription activation complex Deposited 2020-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain G 1–278（278 aa） Chain I 1–278（278 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2 P4P TETRAPHENYLPHOSPHONIUM × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

16 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3d6y
Deposition date deposition_date	2008-05-20
Structure title title	Crystal structure of R275E mutant of BMRR bound to DNA and berberine
Keywords keywords	MULTIDRUG RESISTANCE, TRANSCRIPTION REGULATION, PROTEIN-DNA COMPLEX, Activator, DNA-binding, TRANSCRIPTION REGULATOR-DNA COMPLEX; TRANSCRIPTION REGULATOR/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.57 Å
Radius of gyration Rg (electron density) rg_electron	32.22 Å
Forward intensity I(0) i0	31128000.00
Molecular weight molecular_weight	40315.0 kDa
Excluded volume excluded_volume	48997 Å³
Envelope volume envelope_volume	74571 Å³
Hydration-shell volume shell_volume	20901 Å³
Envelope diameter envelope_diameter	110.2 Å
Shell Rg shell_rg	36.13 Å
Envelope Rg envelope_rg	31.07 Å
Shape Rg shape_rg	32.22 Å
Total Rg total_rg	32.59 Å
Total atoms total_atoms	2813
Residues n_residues	301
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	109.0 Å
Rg (real space) rg_real	32.80 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	3.1130e+07
I(0) uncertainty (real space) i0_real_error	4.7880e+05
Rg (reciprocal space) rg_reciprocal	32.71 Å
I(0) (reciprocal space) i0_reciprocal	31130000.0000
Solution quality estimate total_estimate	0.8665
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.314
Kurtosis Kurtosis kurtosis	-0.692
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2046000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.735; Smooth: 0.900

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

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	B
Atom count atom_count	2847

TGACCCTCCCCTTAGGGGAGGGTC

Entity 2 Entity 2 polymer

Description description	Multidrug-efflux transporter 1 regulator
Molecular weight formula_weight	33450.1 kDa
Mutation mutation	R275E, A277L, E278D
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MKESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIEILDHHHHHH

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	BERBERINE
Molecular weight formula_weight	336.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d6ya1
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	d3d6ya2
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	3d6yA01
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	3d6yA02
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	3d6yA03
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	106.330 Å
Unit-cell length b length_b	106.330 Å
Unit-cell length c length_c	146.750 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	2.700 Å
Low-resolution limit resolution_low	86.100 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2590

fit	/app/data/saxs_computation/d6/3d6y/3d6y.fit
pddf	/app/data/pr_computation/d6/3d6y/3d6y.pr.out
profile	/app/data/saxs_computation/d6/3d6y/3d6y.dat

Crystal structure of R275E mutant of BMRR bound to DNA and berberine

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)