SAXSdb — 9rdr

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

Berberine bridge enzyme-like A

Nicotiana tabacum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[3-[(2~{S})-1-methylpyrrolidin-2-yl]pyridin-1-yl]oxane-3,4,5-triol × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FLAVIN-ADENINE DINUCLEOTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[3-[(2~{S})-1-methylpyrrolidin-2-yl]pyridin-1-yl]oxane-3,4,5-triol × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BBLA_TOBAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–560； UniProt 2–559 Author chain B； PDBConstruct 3–560； UniProt 2–559

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	9rdr
Deposition date deposition_date	2025-06-03
Last revision last_revision	2026-04-22
Structure title title	Nicotine Glucoside Synthase (BBL) in complex with FAD and Nicotine Glucoside
Keywords keywords	Nicotine, FAD, BBL, Oxidoreductase; OXIDOREDUCTASE
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.

9rdr__assembly_1__model_1

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

Download this curve (.dat)

9rdr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rdr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.54 Å
Rg (electron density)	22.69 Å
Total Rg	23.73 Å
Atom count	4093
Residues	504
Excluded volume	72845 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rdr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9rdr__assembly_2__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	Berberine bridge enzyme-like A
Molecular weight formula_weight	62311.7 kDa
EC 编号 ec_number	1.1.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8323

MGFPLIILISFSLASLSETATGAVTNLSACLINHNVHNFSIYPTSRNYFNLLHFSLQNLRFAAPFMPKPTFIILPSSKEELVSTIFCCRKASYEIRVRCGGHSYEGTSYVSFDASPFVIVDLMKLDDVSVDLDSETAWAQGGATIGQIYYAIAKVSDVHAFSAGSGPTVGSGGHISGGGFGLLSRKFGLAADNVVDALLIDADGRLLDRKAMGEDVFWAIRGGGGGNWGIVYAWKIRLLKVPKIVTTCMIYRPGSKQYVAQILEKWQIVTPNLVDDFTLGVLLRPADLPADMKYGNTTPIEIFPQFNALYLGPKTEVLSISNETFPELGVKNDECKEMTWVESALFFSELADVNGNSTGDISRLKERYMDGKGFFKGKTDYVKKPVSMDGMLTFLVELEKNPKGYLVFDPYGGAMDKISDQAIAFPHRKGNLFAIQYLAQWNEEDDYMSDVYMEWIRGFYNTMTPFVSSSPRGAYINYLDMDLGVNMVDDYLLRNASSSSPSSSVDAVERARAWGEMYFLHNYDRLVKAKTQIDPLNVFRHEQSIPPMLGSTQEHKYSSE

Source Source

Source organism organism	Nicotiana tabacum
Common name common_name	common tobacco
NCBI taxonomy ID ncbi_taxonomy_id	4097
Host organism host_organism	Komagataella phaffii

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[3-[(2~{S})-1-methylpyrrolidin-2-yl]pyridin-1-yl]oxane-3,4,5-triol
Molecular weight formula_weight	325.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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Unit-cell length a length_a	84.263 Å
Unit-cell length b length_b	122.880 Å
Unit-cell length c length_c	148.746 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.560 Å
Low-resolution limit resolution_low	74.480 Å
R factor r_factor	0.2153
R_work r_work	0.2126
R_free r_free	0.2693

Nicotine Glucoside Synthase (BBL) in complex with FAD and Nicotine Glucoside

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

Berberine bridge enzyme-like A

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

9rdr__assembly_1__model_1

9rdr__assembly_1__model_1 | I(q)

9rdr__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Nicotine Glucoside Synthase (BBL) in complex with FAD and Nicotine Glucoside

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

Berberine bridge enzyme-like A

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

9rdr__assembly_1__model_1

9rdr__assembly_1__model_1 | I(q)

9rdr__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)