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9qz7

;Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A structure in complex with 2-methylglyceryl-CoA and inactive cofactor 3-deaza-ThDP ;

Method: X-RAY DIFFRACTION D_max: 107.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qz7
deposition_date	2025-04-22
last_revision	2026-02-04
title	;Actinobacterial 2-hydroxyacyl-CoA lyase (AcHACL) mutant E493A 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	31.40 Å
rg_electron	30.74 Å
i0	499957000.00
molecular_weight	116080.0 kDa
excluded_volume	109790 Å³
envelope_volume	181390 Å³
shell_volume	47674 Å³
envelope_diameter	114.7 Å
shell_rg	39.12 Å
envelope_rg	31.10 Å
shape_rg	30.74 Å
total_rg	31.19 Å
total_atoms	8775
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	107.8 Å
rg_real	31.35 Å
rg_real_error	0.98 Å
i0_real	5.0000e+08
i0_real_error	9.1900e+06
rg_reciprocal	31.37 Å
i0_reciprocal	500000000.0000
total_estimate	0.8631
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.8 Å
skewness	0.372
kurtosis	-0.144
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	139700000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.926

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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	65304.1 kDa
ec_number	4.1.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9841

MASHHHHHHSGMADRQDAERSGAGPARQSVPVASLVAEFLQEHGVDRVFGLQGGHIQPIWDQLARRGVRIVDVRDEGSAVHMAHAHTELTGQTAVAMVTAGPGVTNTVTAVANASVSRIPLLVIGGCPPIPQSNMGPLQDIPHTAILEPITRLARTLRSADQVLREFDEAWARASGDRGEPGPVYLEIPTDVLRRDVPPALQMREHLRAKPKRRPQPHPDDVAAVADLIRAAEKPAIISGRGARTTDGTDLVRLLDASGAAYLDTQESRGLVPDSHPAAVGSARSAVMRDTDLLITVGRQLDYQLGMGSPAVFPHAKVVRIADTASELIDNRRGEVEILAEPGAALAAIADALKDHTPDTSWRDELKAKHRKRAEDYRQALHSTENGADGHIHPNRIFGALDALDGDVLDLGETIMIADGGDLLSFGRLGITKARRYLDAGAFGCLGVATPFAIGAALAYPDRPVVAVTGDGAFGITATEIDTAVRHDAKIVVIVSNNRAWNIARYDQAENYGLVVGTDLADSDYAGVARAFGAHGERVTDPAELEGAIRRALANAPALVDVVTTQDAASPDSGKGLGFVPDYQALTPWNDAEVARRQEGIGSAWSHPQFEK

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	1043

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6. Citations (1)

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length_a	103.857 Å
length_b	145.789 Å
length_c	174.337 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	1.720 Å
resolution_low	87.168 Å
r_factor	—
r_work	0.1618
r_free	0.2036

fit	/app/data/saxs_computation/qz/9qz7/9qz7.fit
pddf	/app/data/pr_computation/qz/9qz7/9qz7.pr.out
profile	/app/data/saxs_computation/qz/9qz7/9qz7.dat