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9rdr

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

Method: X-RAY DIFFRACTION D_max: 110.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rdr
deposition_date	2025-06-03
last_revision	2026-04-22
title	Nicotine Glucoside Synthase (BBL) in complex with FAD and Nicotine Glucoside
keywords	Nicotine, FAD, BBL, Oxidoreductase; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	33.85 Å
rg_electron	33.52 Å
i0	392166000.00
molecular_weight	108120.0 kDa
excluded_volume	105260 Å³
envelope_volume	174350 Å³
shell_volume	42979 Å³
envelope_diameter	118.1 Å
shell_rg	40.26 Å
envelope_rg	33.67 Å
shape_rg	33.49 Å
total_rg	33.92 Å
total_atoms	8182
n_residues	1007
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	110.8 Å
rg_real	33.92 Å
rg_real_error	0.79 Å
i0_real	3.9220e+08
i0_real_error	6.0100e+06
rg_reciprocal	33.88 Å
i0_reciprocal	392200000.0000
total_estimate	0.8787
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.0 Å
skewness	0.393
kurtosis	-0.458
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	73670000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.874

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Berberine bridge enzyme-like A
formula_weight	62311.7 kDa
ec_number	1.1.1.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8323

MGFPLIILISFSLASLSETATGAVTNLSACLINHNVHNFSIYPTSRNYFNLLHFSLQNLRFAAPFMPKPTFIILPSSKEELVSTIFCCRKASYEIRVRCGGHSYEGTSYVSFDASPFVIVDLMKLDDVSVDLDSETAWAQGGATIGQIYYAIAKVSDVHAFSAGSGPTVGSGGHISGGGFGLLSRKFGLAADNVVDALLIDADGRLLDRKAMGEDVFWAIRGGGGGNWGIVYAWKIRLLKVPKIVTTCMIYRPGSKQYVAQILEKWQIVTPNLVDDFTLGVLLRPADLPADMKYGNTTPIEIFPQFNALYLGPKTEVLSISNETFPELGVKNDECKEMTWVESALFFSELADVNGNSTGDISRLKERYMDGKGFFKGKTDYVKKPVSMDGMLTFLVELEKNPKGYLVFDPYGGAMDKISDQAIAFPHRKGNLFAIQYLAQWNEEDDYMSDVYMEWIRGFYNTMTPFVSSSPRGAYINYLDMDLGVNMVDDYLLRNASSSSPSSSVDAVERARAWGEMYFLHNYDRLVKAKTQIDPLNVFRHEQSIPPMLGSTQEHKYSSE

Source

organism	Nicotiana tabacum
common_name	common tobacco
ncbi_taxonomy_id	4097
host_organism	Komagataella phaffii

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	8

Entity 5 non-polymer

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
formula_weight	325.4 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	141

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6. Citations (1)

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length_a	84.263 Å
length_b	122.880 Å
length_c	148.746 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.560 Å
resolution_low	74.480 Å
r_factor	0.2153
r_work	0.2126
r_free	0.2693

fit	/app/data/saxs_computation/rd/9rdr/9rdr.fit
pddf	/app/data/pr_computation/rd/9rdr/9rdr.pr.out
profile	/app/data/saxs_computation/rd/9rdr/9rdr.dat