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9s4y

AcuB from Geobacillus stearothermophilus with Ap4A

Method: X-RAY DIFFRACTION D_max: 81.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s4y
deposition_date	2025-07-28
title	AcuB from Geobacillus stearothermophilus with Ap4A
keywords	Repressor, acetoin utilization operon, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	24.61 Å
rg_electron	23.74 Å
i0	36793500.00
molecular_weight	46395.0 kDa
excluded_volume	58086 Å³
envelope_volume	71629 Å³
shell_volume	25429 Å³
envelope_diameter	82.2 Å
shell_rg	30.77 Å
envelope_rg	24.10 Å
shape_rg	23.76 Å
total_rg	24.53 Å
total_atoms	6584
n_residues	402
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	81.5 Å
rg_real	24.64 Å
rg_real_error	0.53 Å
i0_real	3.6790e+07
i0_real_error	5.4710e+05
rg_reciprocal	24.64 Å
i0_reciprocal	36790000.0000
total_estimate	0.8843
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.9 Å
skewness	0.392
kurtosis	-0.327
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	11720000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	AcuB from Geobacillus stearothermophilus
formula_weight	24765.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6599

ALVEQAMKAPVITLRATNTIAEALQLLRHHRIRHLPVVDGEGRLLGLVTSQDLRDASPSIFHLHEHLEDLQKPVSTIMKTDLIVGHPLDFVEEVAALFYEHRIGCLPIVNHGKLVGIITQTDLLRTFIELTGVHQPGSQIEIKVPNEAGMLSKAAAIISERHVNIASVLVYPAPDPNEKILVFRVQTMNPLPLIRDLQNAGYHVLWPNLPGVTSGSSHHHHHH

Source

organism	Bacillus subtilis subsp. subtilis str. 168
ncbi_taxonomy_id	224308
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	BIS(ADENOSINE)-5'-TETRAPHOSPHATE
formula_weight	836.4 kDa
src_method	man
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	52.295 Å
length_b	96.954 Å
length_c	101.709 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	3.350 Å
resolution_low	48.524 Å
r_factor	—
r_work	0.2288
r_free	0.2617

fit	/app/data/saxs_computation/s4/9s4y/9s4y.fit
pddf	/app/data/pr_computation/s4/9s4y/9s4y.pr.out
profile	/app/data/saxs_computation/s4/9s4y/9s4y.dat

AcuB from Geobacillus stearothermophilus with Ap4A

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