← Back to search

9s5k

ADC-30 class C beta-lactamase in a di-covalent complex with benzoxaborole AK-431

Method: X-RAY DIFFRACTION D_max: 97.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9s5k
deposition_date	2025-07-29
last_revision	2025-09-17
title	ADC-30 class C beta-lactamase in a di-covalent complex with benzoxaborole AK-431
keywords	complex, boronate, di-covalent, antibiotic resistance, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.75 Å
rg_electron	30.23 Å
i0	98975800.00
molecular_weight	81105.0 kDa
excluded_volume	102510 Å³
envelope_volume	124060 Å³
shell_volume	34422 Å³
envelope_diameter	101.0 Å
shell_rg	37.11 Å
envelope_rg	30.02 Å
shape_rg	30.22 Å
total_rg	30.90 Å
total_atoms	5718
n_residues	717
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

▼

3. P(r) Analysis (GNOM)

dmax	97.7 Å
rg_real	30.80 Å
rg_real_error	0.55 Å
i0_real	9.8980e+07
i0_real_error	1.3800e+06
rg_reciprocal	30.78 Å
i0_reciprocal	98970000.0000
total_estimate	0.8948
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	30.1 Å
skewness	0.323
kurtosis	-0.641
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	27330000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.937

▶

4. Crystallography & Experiment

▶

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	6842

SNTPKDQEIKKLVDQNFKPLLEKYDVPGMAVGVIQNNKKYEMYYGLQSVQDKKAVNSSTIFELGSVSKLFTATAGGYAKNKGKISFDDTPGKYWKELKNTPIDQVNLLQLATYTSGNLALQFPDEVKTDQQVLTFFKDWKPKNSIGEYRQYSNPSIGLFGKVVALSMNKPFDQVLEKTIFPALGLKHSYVNVPKTQMQNYAFGYNQENQPIRVNPGPLDAPAYGVKSTLPDMLSFIHANLNPQKYPADIQRAINETHQGRYQVNTMYQALGWEEFSYPATLQTLLDSNSEQIVMKPNKVTAISKEPSVKMYHKTGSTTGFGTYVVFIPKENIGLVMLTNKRIPNEERIKAAYAVLNAIKK

Source

organism	Acinetobacter baumannii
ncbi_taxonomy_id	470
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	2-[(9~{R})-8-oxa-7-boranidabicyclo[4.3.0]nona-1,3,5-trien-9-yl]ethanoic acid
formula_weight	175.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCINE
formula_weight	75.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	958

▶

6. Citations (1)

▶

length_a	43.381 Å
length_b	83.545 Å
length_c	208.316 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	orthorhombic

resolution	1.380 Å
resolution_low	52.080 Å
r_factor	0.1659
r_work	0.1649
r_free	0.1853

fit	/app/data/saxs_computation/s5/9s5k/9s5k.fit
pddf	/app/data/pr_computation/s5/9s5k/9s5k.pr.out
profile	/app/data/saxs_computation/s5/9s5k/9s5k.dat