← Back to search

9qz4

;Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493D structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP ;

Method: X-RAY DIFFRACTION D_max: 104.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qz4
deposition_date	2025-04-22
last_revision	2026-02-04
title	;Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493D structure in complex with substrate 2-HIB-CoA and inactive cofactor 3-deaza-ThDP ;
keywords	ThDP, CoA, HACL, LYASE; LYASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	31.59 Å
rg_electron	30.70 Å
i0	264426000.00
molecular_weight	124780.0 kDa
excluded_volume	153870 Å³
envelope_volume	180780 Å³
shell_volume	47554 Å³
envelope_diameter	114.5 Å
shell_rg	39.10 Å
envelope_rg	31.10 Å
shape_rg	30.71 Å
total_rg	31.26 Å
total_atoms	8773
n_residues	1147
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

▼

3. P(r) Analysis (GNOM)

dmax	104.9 Å
rg_real	31.54 Å
rg_real_error	0.86 Å
i0_real	2.6440e+08
i0_real_error	4.0210e+06
rg_reciprocal	31.56 Å
i0_reciprocal	264400000.0000
total_estimate	0.8030
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.8 Å
skewness	0.365
kurtosis	-0.154
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	118200000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	2-hydroxyacyl-CoA lyase
formula_weight	65348.1 kDa
ec_number	4.1.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9764

MASHHHHHHSGMADRQDAERSGAGPARQSVPVASLVAEFLQEHGVDRVFGLQGGHIQPIWDQLARRGVRIVDVRDEGSAVHMAHAHTELTGQTAVAMVTAGPGVTNTVTAVANASVSRIPLLVIGGCPPIPQSNMGPLQDIPHTAILEPITRLARTLRSADQVLREFDEAWARASGDRGEPGPVYLEIPTDVLRRDVPPALQMREHLRAKPKRRPQPHPDDVAAVADLIRAAEKPAIISGRGARTTDGTDLVRLLDASGAAYLDTQESRGLVPDSHPAAVGSARSAVMRDTDLLITVGRQLDYQLGMGSPAVFPHAKVVRIADTASELIDNRRGEVEILAEPGAALAAIADALKDHTPDTSWRDELKAKHRKRAEDYRQALHSTENGADGHIHPNRIFGALDALDGDVLDLGETIMIADGGDLLSFGRLGITKARRYLDAGAFGCLGVATPFAIGAALAYPDRPVVAVTGDGAFGITATEIDTAVRHDAKIVVIVSNNRAWNIDRYDQAENYGLVVGTDLADSDYAGVARAFGAHGERVTDPAELEGAIRRALANAPALVDVVTTQDAASPDSGKGLGFVPDYQALTPWNDAEVARRQEGIGSAWSHPQFEK

Source

organism	Actinomycetospora chiangmaiensis DSM 45062
ncbi_taxonomy_id	1120948
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
formula_weight	423.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	;S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxy-2-methylpropanethioate ;
formula_weight	853.6 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	991

▶

6. Citations (1)

▶

length_a	103.980 Å
length_b	147.528 Å
length_c	174.449 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.630 Å
resolution_low	87.225 Å
r_factor	—
r_work	0.1574
r_free	0.1928

fit	/app/data/saxs_computation/qz/9qz4/9qz4.fit
pddf	/app/data/pr_computation/qz/9qz4/9qz4.pr.out
profile	/app/data/saxs_computation/qz/9qz4/9qz4.dat