SAXSdb — 9rgu

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1. Structure Basics

entry_id	9rgu
deposition_date	2025-06-07
last_revision	2026-05-13
title	;Crystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in complex with 3S hydroxyhexanoyl-PAN and 3',5', diphosphate adenosine ;
keywords	crotonase, hydratase, beta-oxidation, LYASE; LYASE
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	33.02 Å
rg_electron	32.01 Å
i0	871927000.00
molecular_weight	156430.0 kDa
excluded_volume	149590 Å³
envelope_volume	256470 Å³
shell_volume	61669 Å³
envelope_diameter	99.6 Å
shell_rg	42.29 Å
envelope_rg	31.95 Å
shape_rg	32.01 Å
total_rg	32.54 Å
total_atoms	11773
n_residues	1518
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	96.7 Å
rg_real	32.59 Å
rg_real_error	0.13 Å
i0_real	8.3960e+08
i0_real_error	9.1010e+06
rg_reciprocal	32.82 Å
i0_reciprocal	872000000.0000
total_estimate	0.7287
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	44.3 Å
skewness	-0.001
kurtosis	-0.559
angular_range	— – 0.2400 Å⁻¹
current_alpha	4.6630
highest_alpha	144700000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 0.912; Sysdev: 0.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Enoyl-CoA hydratase, mitochondrial
formula_weight	31587.4 kDa
ec_number	4.2.1.17,5.3.3.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,F
atom_count	12437

MAALRALLPRACNSLLSPVRCPEFRRFASGANFQYIITEKKGKNSSVGLIQLNRPKALNALCNGLIEELNQALETFEEDPAVGAIVLTGGEKAFAAGADIKEMQNRTFQDCYSGKFLSHWDHITRIKKPVIAAVNGYALGGGCELAMMCDIIYAGEKAQFGQPEILLGTIPGAGGTQRLTRAVGKSLAMEMVLTGDRISAQDAKQAGLVSKIFPVETLVEEAIQCAEKIANNSKIIVAMAKESVNAAFEMTLTEGNKLEKKLFYSTFATDDRREGMSAFVEKRKANFKDH

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Enoyl-CoA hydratase, mitochondrial
formula_weight	31571.4 kDa
ec_number	4.2.1.17,5.3.3.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,C

MAALRALLPRACNSLLSPVRCPEFRRFASGANFQYIITEKKGKNSSVGLIQLNRPKALNALCNGLIEELNQALETFEEDPAVGAIVLTGGEKAFAAGADIKEMQNRTFQDCYSGKFLSHWDHITRIKKPVIAAVNGYALGGGCELAMMCDIIYAGEKAQFGQPEILLGTIPGAGGTQRLTRAVGKSLAMEMVLTGDRISAQDAKQAGLVSKIFPVETLVEEAIQCAEKIANNSKIIVAMAKESVNAAFEMTLTEGNKLEKKLFYSTFATDDRREGMSAFVEKRKANFKDH

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Enoyl-CoA hydratase, mitochondrial
formula_weight	31587.4 kDa
ec_number	4.2.1.17,5.3.3.8
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MAALRALLPRACNSLLSPVRCPEFRRFASGANFQYIITEKKGKNSSVGLIQLNRPKALNALCNGLIEELNQALETFEEDPAVGAIVLTGGEKAFAAGADIKEMQNRTFQDCYSGKFLSHWDHITRIKKPVIAAVNGYALGGGCELAMMCDIIYAGEKAQFGQPEILLGTIPGAGGTQRLTRAVGKSLAMEMVLTGDRISAQDAKQAGLVSKIFPVETLVEEAIQCAEKIANNSKIIVAMAKESVNAAFEMTLTEGNKLEKKLFYSTFATDDRREGMSAFVEKRKANFKDH

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli BL21(DE3)

Entity 4 polymer

description	Enoyl-CoA hydratase, mitochondrial
formula_weight	31571.4 kDa
ec_number	4.2.1.17,5.3.3.8
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MAALRALLPRACNSLLSPVRCPEFRRFASGANFQYIITEKKGKNSSVGLIQLNRPKALNALCNGLIEELNQALETFEEDPAVGAIVLTGGEKAFAAGADIKEMQNRTFQDCYSGKFLSHWDHITRIKKPVIAAVNGYALGGGCELAMMCDIIYAGEKAQFGQPEILLGTIPGAGGTQRLTRAVGKSLAMEMVLTGDRISAQDAKQAGLVSKIFPVETLVEEAIQCAEKIANNSKIIVAMAKESVNAAFEMTLTEGNKLEKKLFYSTFATDDRREGMSAFVEKRKANFKDH

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli BL21(DE3)

Entity 5 non-polymer

description	COENZYME A
formula_weight	767.5 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2,4-bis(oxidanyl)butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanylhexanethioate
formula_weight	392.5 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	ADENOSINE-3'-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	4

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	490

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6. Citations (1)

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length_a	75.833 Å
length_b	92.997 Å
length_c	247.469 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.700 Å
resolution_low	47.900 Å
r_factor	—
r_work	0.2170
r_free	0.2476

fit	/app/data/saxs_computation/rg/9rgu/9rgu.fit
pddf	/app/data/pr_computation/rg/9rgu/9rgu.pr.out
profile	/app/data/saxs_computation/rg/9rgu/9rgu.dat

;Crystal Structure of Rattus norvegicus Enoyl-CoA Hydratase in complex with 3S hydroxyhexanoyl-PAN and 3',5', diphosphate adenosine ;

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)