SAXSdb — 9vco

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1. Structure Basics

entry_id	9vco
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	34.23 Å
rg_electron	33.40 Å
i0	222466000.00
molecular_weight	117410.0 kDa
excluded_volume	145950 Å³
envelope_volume	188700 Å³
shell_volume	46885 Å³
envelope_diameter	110.6 Å
shell_rg	40.56 Å
envelope_rg	32.89 Å
shape_rg	33.37 Å
total_rg	34.01 Å
total_atoms	8293
n_residues	1150
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	109.4 Å
rg_real	34.12 Å
rg_real_error	0.77 Å
i0_real	2.2250e+08
i0_real_error	3.7300e+06
rg_reciprocal	34.19 Å
i0_reciprocal	222500000.0000
total_estimate	0.6992
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	40.4 Å
skewness	0.175
kurtosis	-0.567
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	46290000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 0.122; Positv: 1.000; Valcen: 0.998; Smooth: 0.925

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	8527

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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	234

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6. Citations (1)

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length_a	191.651 Å
length_b	81.901 Å
length_c	88.649 Å
angle_alpha	90.00 °
angle_beta	100.57 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.290 Å
resolution_low	42.640 Å
r_factor	0.1953
r_work	0.1939
r_free	0.2373

fit	/app/data/saxs_computation/vc/9vco/9vco.fit
pddf	/app/data/pr_computation/vc/9vco/9vco.pr.out
profile	/app/data/saxs_computation/vc/9vco/9vco.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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)