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9w16

3-hydroxybutyryl-CoA dehydrogenase with NAD

Method: X-RAY DIFFRACTION D_max: 119.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w16
deposition_date	2025-07-25
last_revision	2026-04-15
title	3-hydroxybutyryl-CoA dehydrogenase with NAD
keywords	NAD complex, 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	37.88 Å
rg_electron	37.06 Å
i0	508625000.00
molecular_weight	186640.0 kDa
excluded_volume	235320 Å³
envelope_volume	302660 Å³
shell_volume	65302 Å³
envelope_diameter	123.3 Å
shell_rg	44.92 Å
envelope_rg	37.02 Å
shape_rg	37.06 Å
total_rg	37.54 Å
total_atoms	13010
n_residues	1740
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	119.3 Å
rg_real	37.61 Å
rg_real_error	0.92 Å
i0_real	5.0860e+08
i0_real_error	8.8800e+06
rg_reciprocal	37.78 Å
i0_reciprocal	508700000.0000
total_estimate	0.8144
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.1 Å
skewness	0.110
kurtosis	-0.413
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	64560000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein
formula_weight	31109.4 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	D,F,E,C,B,A
atom_count	13048

MKIGVIGAGTMGQGIAKAFAQVEGNTVALCDIKQEWAENGLKKIKGGYDKLVAKGKMTQEKADAIVAAITPGLKEDLCADCDLVVEAAFEDMKVKQTTFGELDKICKPECIFASNTSSLSITEIGKGLSRPMIGMHFFNPADRMKLIEVIAGCNTPAETVEKIKEISVAIGKSPVQVNEAAGFVVNRILIPMINEAAFIKMEGVSNIAGIDTAMKLGANHPMGPLELGDFIGLDICLAIMDVLYKETGDSKYRACPLIRKMVRGGNLGCKSGKGFYVYNADRTKTPVDEL

Source

organism	Faecalibacterium prausnitzii L2-6
ncbi_taxonomy_id	718252
host_organism	Escherichia coli

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	38

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6. Citations (1)

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length_a	82.963 Å
length_b	147.782 Å
length_c	167.444 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.710 Å
resolution_low	47.260 Å
r_factor	0.2229
r_work	0.2213
r_free	0.2632

fit	/app/data/saxs_computation/w1/9w16/9w16.fit
pddf	/app/data/pr_computation/w1/9w16/9w16.pr.out
profile	/app/data/saxs_computation/w1/9w16/9w16.dat

3-hydroxybutyryl-CoA dehydrogenase with NAD

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