SAXSdb — 9vcn

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1. Structure Basics

entry_id	9vcn
deposition_date	2025-06-06
last_revision	2026-06-10
title	NAD-DEPENDENT DEHYDROGENASE
keywords	DEHYDROGENASE, COMPLEX, NAD-DEPENDENT, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	34.00 Å
rg_electron	33.33 Å
i0	437152000.00
molecular_weight	111120.0 kDa
excluded_volume	106630 Å³
envelope_volume	189090 Å³
shell_volume	46970 Å³
envelope_diameter	111.3 Å
shell_rg	40.52 Å
envelope_rg	32.91 Å
shape_rg	33.29 Å
total_rg	33.77 Å
total_atoms	8434
n_residues	1151
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	107.1 Å
rg_real	33.90 Å
rg_real_error	0.94 Å
i0_real	4.3720e+08
i0_real_error	7.9810e+06
rg_reciprocal	33.96 Å
i0_reciprocal	437200000.0000
total_estimate	0.9033
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	41.0 Å
skewness	0.179
kurtosis	-0.564
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	56000000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.906

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	NADH-dependent dihydrogenase
formula_weight	35368.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	8640

MAPTGGVGESRYVKTLRQLEVALIGAGLIARLHLEAWLGAGAAVRVYSDDGRSRELAAEFGAKAAGSLEEALDGADAVDICTPTASHHEIALTAIAAGVGVVCEKPLAASAEEAEEIVTAAERAGVRLYAAHDVRFAAPYARLHELVASGRLGEGALGRFSFSAYHPRPWTGHASARSGGILTDQLLHGADLAHWVFGDVVRVHACYQGDIATPAPEGAVATGTAVLTHASGAISQVVSRWTATPRPPVRVAFHVSGTGGSVSYDSEWPQEVRVVDGGAGNFAYGGPSVFDTEMREFATAFAGGPEPRIGAKDALAAVRIIHAAAESAWTGRAVELPVRGAA

Source

organism	Amycolatopsis mediterranei S699
ncbi_taxonomy_id	713604
host_organism	Escherichia coli

Entity 2 polymer

description	RifT
formula_weight	26214.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MVKVAILSSTPQAYAGALRGLPDVEVVAAASWDAFEPVRQAAEAGARVLCEYPPAAKETDLKAMIDAAGDRLTFASPACHGEAFAVVRKGIADGGIGELTTVLGSVATSVDGVLGAAAPYLLDLADAVLGGEPAQQVYAQTNIVLSGRIGESAAVLTVRYRSGQVASFDCRRHGSATGLPAVTFIGDQGSVQYDAGPQLLGGERPELGGEDLEALMLKDFLGAGDGPGPDGQAALRTFRIIQAAYESAHTGQPVDL

Source

organism	Amycolatopsis mediterranei S699
ncbi_taxonomy_id	713604
host_organism	Escherichia coli

Entity 3 non-polymer

description	;(7E,9S,10S,11R,12R,13R,14R,15R,16S,17S,18E,20Z)-2,4,10,12,14,16-hexahydroxy-3,7,9,11,13,15,17,21-octamethyl-23-azatricyclo[22.3.1.05,27]octacosa-1,3,5(27),7,18,20,24-heptaene-6,22,26,28-tetrone ;
formula_weight	639.7 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	206

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6. Citations (1)

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length_a	190.854 Å
length_b	82.354 Å
length_c	88.277 Å
angle_alpha	90.00 °
angle_beta	100.04 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.390 Å
resolution_low	46.980 Å
r_factor	0.1959
r_work	0.1938
r_free	0.2502

fit	/app/data/saxs_computation/vc/9vcn/9vcn.fit
pddf	/app/data/pr_computation/vc/9vcn/9vcn.pr.out
profile	/app/data/saxs_computation/vc/9vcn/9vcn.dat

NAD-DEPENDENT DEHYDROGENASE

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)