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9s5l

ADC-30 class C beta-lactamase in complex with benzoxaborole AK-412

Method: X-RAY DIFFRACTION D_max: 105.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s5l
deposition_date	2025-07-29
last_revision	2025-09-17
title	ADC-30 class C beta-lactamase in complex with benzoxaborole AK-412
keywords	complex, boronate, covalent, antibiotic resistance, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL 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	32.06 Å
rg_electron	31.81 Å
i0	192649000.00
molecular_weight	75643.0 kDa
excluded_volume	73895 Å³
envelope_volume	124180 Å³
shell_volume	33347 Å³
envelope_diameter	109.2 Å
shell_rg	37.67 Å
envelope_rg	31.63 Å
shape_rg	31.78 Å
total_rg	32.22 Å
total_atoms	5763
n_residues	716
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	105.9 Å
rg_real	32.27 Å
rg_real_error	0.68 Å
i0_real	1.9260e+08
i0_real_error	2.9940e+06
rg_reciprocal	32.19 Å
i0_reciprocal	192600000.0000
total_estimate	0.8536
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	28.1 Å
skewness	0.412
kurtosis	-0.629
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0001
highest_alpha	34390000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.844; Smooth: 0.905

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Beta-lactamase
formula_weight	40569.2 kDa
ec_number	3.5.2.6
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	6618

SNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK

Source

organism	Acinetobacter baumannii
ncbi_taxonomy_id	470
host_organism	Escherichia coli

Entity 2 non-polymer

description	4-chloranyl-N-[[(3S)-1-oxidanyl-3H-2,1$l^{4}-benzoxaborol-3-yl]methyl]benzenesulfonamide
formula_weight	337.6 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	752

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6. Citations (1)

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length_a	45.560 Å
length_b	176.460 Å
length_c	49.440 Å
angle_alpha	90.00 °
angle_beta	111.99 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.600 Å
resolution_low	42.250 Å
r_factor	0.1707
r_work	0.1690
r_free	0.2024

fit	/app/data/saxs_computation/s5/9s5l/9s5l.fit
pddf	/app/data/pr_computation/s5/9s5l/9s5l.pr.out
profile	/app/data/saxs_computation/s5/9s5l/9s5l.dat