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9ta3

Cryo-EM structure of Heyndrickxia coagulans beta-galactosidase

Method: ELECTRON MICROSCOPY D_max: 146.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ta3
deposition_date	2025-11-18
title	Cryo-EM structure of Heyndrickxia coagulans beta-galactosidase
keywords	beta-galactosidase, Heyndrickxia coagulans, transgalactosylation, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

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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	49.86 Å
rg_electron	49.14 Å
i0	2830460000.00
molecular_weight	451950.0 kDa
excluded_volume	566580 Å³
envelope_volume	720800 Å³
shell_volume	117210 Å³
envelope_diameter	148.5 Å
shell_rg	58.41 Å
envelope_rg	46.87 Å
shape_rg	49.10 Å
total_rg	49.53 Å
total_atoms	31914
n_residues	3954
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	146.9 Å
rg_real	49.59 Å
rg_real_error	0.89 Å
i0_real	2.8300e+09
i0_real_error	4.9800e+07
rg_reciprocal	50.07 Å
i0_reciprocal	2832000000.0000
total_estimate	0.8733
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	68.9 Å
skewness	0.006
kurtosis	-0.572
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	178200000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.514

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Beta-galactosidase LacZ
formula_weight	76938.2 kDa
ec_number	3.2.1.23
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	32352

MLKKHEKFYYGGDYNPEQWDESVWKEDMRLMKKAGVNYVSINIFSWARLQPDEETYDFSTLDKIMDMLAENGIGVDLATATAAPPAWLSRKYPDSLPVDKDGSRFLPGSRQHYCPNSKDYARLAAKLVRKIAERYKSHPALVMWHVNNEYGCHISECYCDNCKKGFQTWLKEKYGTIENLNKSWSTDFWSQRYYEWEEICLPGKTPTFANPMQQLDYKAFMDDSLLALYKMERDILKAYTPDVPVMTNLMGLHKPVDGFHWAKEMDLVTWDAYPDPFEDIPYAQFMAHDLTRSLKKQPFLLMEQAAGAVNWRAQNAVKAPGVMRLWSYEAAAHGADGIMFFQWRASQGGAEKFHSGMVPHSGDEESRNFREVVQLGNELKNLEKVTGSAYASDVAIVFDWKNWWALELDSKPSSLVTYIKQLLPFYRVLHTQNIGVDFIHPDEAMDRYKVVFAPASYRVTKTFADKVKAYVENGGYFATNFFSGIADENERVYLGGYPGAYRDILGIYVEEFAPMKKGAVHQIRTGYGDAAIRVWEEKIHLKGAEALAWFKDGYLAGSPAVTAHHCGKGKAYYIGTQPDEQYLSSLLKEILKEADVRPALDAPRGVEVAVRKNGHEKFLFLLNHTDQVQFVDAGGTYPELIYGRTEAETVRLSPRDVKILQVIEKHHHHHH

Source

organism	Heyndrickxia coagulans
ncbi_taxonomy_id	1398
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	438

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.97 Å
resolution_method	—
num_particles	629632

fit	/app/data/saxs_computation/ta/9ta3/9ta3.fit
pddf	/app/data/pr_computation/ta/9ta3/9ta3.pr.out
profile	/app/data/saxs_computation/ta/9ta3/9ta3.dat