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9s4v

AcuB from Bacillus subtilis with AMP and ADP

Method: X-RAY DIFFRACTION D_max: 102.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s4v
deposition_date	2025-07-28
title	AcuB from Bacillus subtilis with AMP and ADP
keywords	Repressor, adenine nucleotide, DNA BINDING PROTEIN, PROTEIN BINDING; PROTEIN BINDING
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	31.39 Å
rg_electron	30.96 Å
i0	89792500.00
molecular_weight	74901.0 kDa
excluded_volume	94023 Å³
envelope_volume	126090 Å³
shell_volume	35181 Å³
envelope_diameter	109.0 Å
shell_rg	36.53 Å
envelope_rg	31.17 Å
shape_rg	30.98 Å
total_rg	31.39 Å
total_atoms	10632
n_residues	641
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	102.8 Å
rg_real	31.43 Å
rg_real_error	0.84 Å
i0_real	8.9790e+07
i0_real_error	1.3310e+06
rg_reciprocal	31.41 Å
i0_reciprocal	89790000.0000
total_estimate	0.8875
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	39.0 Å
skewness	0.358
kurtosis	-0.280
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	15200000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.815

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Acetoin utilization protein AcuB
formula_weight	25504.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	10661

GMIVEQIMKRDVITLTKTDTLETAICKLKEFHIRHLPVVDEERHVIGMITDRDMKQASPSIFEENKRSLFLTRSVDSIMKKDVVCAHPLDFVEEISAVFYEHGIGCLPVVHHQKLIGILTKTDLLRTFVKLTGADQPGSQIEIKVNDITKSLAEISSLCQDLQVKILSVLVYPHDDPGVKVLVFRVKTMNPLPFLQALQRNGHHVVWPSEQRDLLGSSHHHHHH

Source

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

Entity 2 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	14

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6. Citations (1)

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length_a	67.305 Å
length_b	79.779 Å
length_c	153.788 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 2 21
int_tables_number	18
crystal_system	—

resolution	2.640 Å
resolution_low	48.790 Å
r_factor	—
r_work	0.2067
r_free	0.2664

fit	/app/data/saxs_computation/s4/9s4v/9s4v.fit
pddf	/app/data/pr_computation/s4/9s4v/9s4v.pr.out
profile	/app/data/saxs_computation/s4/9s4v/9s4v.dat

AcuB from Bacillus subtilis with AMP and ADP

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