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9rdd

Nicotinic Acid N-glucoside Reductase NaGR (A622) in complex with NADP+ and Nicotinic Acid N-glucoside

Method: X-RAY DIFFRACTION D_max: 64.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rdd
deposition_date	2025-06-02
last_revision	2026-04-22
title	Nicotinic Acid N-glucoside Reductase NaGR (A622) in complex with NADP+ and Nicotinic Acid N-glucoside
keywords	Nicotine, NADP, 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	20.08 Å
rg_electron	19.28 Å
i0	38149300.00
molecular_weight	32547.0 kDa
excluded_volume	31750 Å³
envelope_volume	48877 Å³
shell_volume	20946 Å³
envelope_diameter	65.5 Å
shell_rg	25.86 Å
envelope_rg	19.53 Å
shape_rg	19.27 Å
total_rg	19.94 Å
total_atoms	2474
n_residues	310
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	64.2 Å
rg_real	20.00 Å
rg_real_error	0.30 Å
i0_real	3.8150e+07
i0_real_error	4.6270e+05
rg_reciprocal	20.02 Å
i0_reciprocal	38150000.0000
total_estimate	0.8974
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.8 Å
skewness	0.233
kurtosis	-0.401
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	7407000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Isoflavone reductase homolog A622
formula_weight	35358.5 kDa
ec_number	1.3.1.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2893

MVVSEKSKILIIGGTGYIGKYLVETSAKSGHPTFALIRESTLKNPEKSKLIDTFKSYGVTLLFGDISNQESLLKAIKQVDVVISTVGGQQFTDQVNIIKAIKEAGNIKRFLPSEFGFDVDHARAIEPAASLFALKVRIRRMIEAEGIPYTYVICNWFADFFLPNLGQLEAKTPPRDKVVIFGDGNPKAIYVKEEDIATYTIEAVDDPRTLNKTLHMRPPANILSFNEIVSLWEDKIGKTLEKLYLSEEDILQIVQEGPLPLRTNLAICHSVFVNGDSANFEVQPPTGVEATELYPKVKYTTVDEFYNKFVLHHHH

Source

organism	Nicotiana tabacum
common_name	common tobacco
ncbi_taxonomy_id	4097
host_organism	Escherichia coli

Entity 2 non-polymer

description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	743.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	N-(beta-D-glucosyl)nicotinate
formula_weight	286.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	406

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6. Citations (1)

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length_a	39.586 Å
length_b	45.531 Å
length_c	53.473 Å
angle_alpha	73.20 °
angle_beta	79.99 °
angle_gamma	69.64 °
z_pdb	1

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.280 Å
resolution_low	51.020 Å
r_factor	0.1711
r_work	0.1691
r_free	0.2101

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

Nicotinic Acid N-glucoside Reductase NaGR (A622) in complex with NADP+ and Nicotinic Acid N-glucoside

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction