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9w15

3-Hydroxybutyryl-CoA dehydrogenase with NAD and acetoacetyl CoA

Method: X-RAY DIFFRACTION D_max: 112.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w15
deposition_date	2025-07-25
last_revision	2026-04-15
title	3-Hydroxybutyryl-CoA dehydrogenase with NAD and acetoacetyl CoA
keywords	NAD and acetoacetyl-CoA 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	37.28 Å
rg_electron	36.38 Å
i0	555144000.00
molecular_weight	191360.0 kDa
excluded_volume	239590 Å³
envelope_volume	302810 Å³
shell_volume	65801 Å³
envelope_diameter	115.6 Å
shell_rg	45.06 Å
envelope_rg	36.45 Å
shape_rg	36.37 Å
total_rg	36.90 Å
total_atoms	13310
n_residues	1734
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	112.7 Å
rg_real	37.00 Å
rg_real_error	0.87 Å
i0_real	5.5510e+08
i0_real_error	9.2910e+06
rg_reciprocal	37.18 Å
i0_reciprocal	555200000.0000
total_estimate	0.8934
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.0 Å
skewness	0.078
kurtosis	-0.499
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	149600000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.856

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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	B,A,C,D,E,F
atom_count	13310

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	4

Entity 3 non-polymer

description	ACETOACETYL-COENZYME A
formula_weight	851.6 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	83.623 Å
length_b	92.142 Å
length_c	132.473 Å
angle_alpha	90.00 °
angle_beta	100.42 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	3.290 Å
resolution_low	48.010 Å
r_factor	0.2557
r_work	0.2526
r_free	0.2940

fit	/app/data/saxs_computation/w1/9w15/9w15.fit
pddf	/app/data/pr_computation/w1/9w15/9w15.pr.out
profile	/app/data/saxs_computation/w1/9w15/9w15.dat

3-Hydroxybutyryl-CoA dehydrogenase with NAD and acetoacetyl CoA

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