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9qz6

Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with 2-methylglyceryl-CoA and inactive cofactor 3-deaza-ThDP

Method: X-RAY DIFFRACTION D_max: 106.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qz6
deposition_date	2025-04-22
last_revision	2026-02-04
title	Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) structure in complex with 2-methylglyceryl-CoA and inactive cofactor 3-deaza-ThDP
keywords	ThDP, CoA, HACL, 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	31.36 Å
rg_electron	30.71 Å
i0	500873000.00
molecular_weight	116190.0 kDa
excluded_volume	109890 Å³
envelope_volume	180990 Å³
shell_volume	47608 Å³
envelope_diameter	114.8 Å
shell_rg	39.09 Å
envelope_rg	31.08 Å
shape_rg	30.71 Å
total_rg	31.16 Å
total_atoms	8783
n_residues	1148
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	106.6 Å
rg_real	31.31 Å
rg_real_error	0.89 Å
i0_real	5.0090e+08
i0_real_error	8.6600e+06
rg_reciprocal	31.34 Å
i0_reciprocal	500900000.0000
total_estimate	0.7904
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	37.6 Å
skewness	0.373
kurtosis	-0.148
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	142900000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	2-hydroxyacyl-CoA lyase
formula_weight	65362.2 kDa
ec_number	4.1.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9873

MASHHHHHHSGMADRQDAERSGAGPARQSVPVASLVAEFLQEHGVDRVFGLQGGHIQPIWDQLARRGVRIVDVRDEGSAVHMAHAHTELTGQTAVAMVTAGPGVTNTVTAVANASVSRIPLLVIGGCPPIPQSNMGPLQDIPHTAILEPITRLARTLRSADQVLREFDEAWARASGDRGEPGPVYLEIPTDVLRRDVPPALQMREHLRAKPKRRPQPHPDDVAAVADLIRAAEKPAIISGRGARTTDGTDLVRLLDASGAAYLDTQESRGLVPDSHPAAVGSARSAVMRDTDLLITVGRQLDYQLGMGSPAVFPHAKVVRIADTASELIDNRRGEVEILAEPGAALAAIADALKDHTPDTSWRDELKAKHRKRAEDYRQALHSTENGADGHIHPNRIFGALDALDGDVLDLGETIMIADGGDLLSFGRLGITKARRYLDAGAFGCLGVATPFAIGAALAYPDRPVVAVTGDGAFGITATEIDTAVRHDAKIVVIVSNNRAWNIERYDQAENYGLVVGTDLADSDYAGVARAFGAHGERVTDPAELEGAIRRALANAPALVDVVTTQDAASPDSGKGLGFVPDYQALTPWNDAEVARRQEGIGSAWSHPQFEK

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	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	;~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (2~{S})-2-methyl-2,3-bis(oxidanyl)propanethioate ;
formula_weight	869.6 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1065

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6. Citations (1)

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length_a	103.768 Å
length_b	146.493 Å
length_c	174.321 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	1.551 Å
resolution_low	84.680 Å
r_factor	—
r_work	0.1577
r_free	0.1841

fit	/app/data/saxs_computation/qz/9qz6/9qz6.fit
pddf	/app/data/pr_computation/qz/9qz6/9qz6.pr.out
profile	/app/data/saxs_computation/qz/9qz6/9qz6.dat