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9s5m

ADC-30 class C beta-lactamase in complex with taniborbactam

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s5m
deposition_date	2025-07-29
last_revision	2025-09-17
title	ADC-30 class C beta-lactamase in complex with taniborbactam
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	30.75 Å
rg_electron	30.17 Å
i0	98858800.00
molecular_weight	81693.0 kDa
excluded_volume	103500 Å³
envelope_volume	124310 Å³
shell_volume	34510 Å³
envelope_diameter	101.0 Å
shell_rg	37.05 Å
envelope_rg	30.00 Å
shape_rg	30.15 Å
total_rg	30.87 Å
total_atoms	5822
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

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3. P(r) Analysis (GNOM)

dmax	97.7 Å
rg_real	30.80 Å
rg_real_error	0.63 Å
i0_real	9.8860e+07
i0_real_error	1.4660e+06
rg_reciprocal	30.78 Å
i0_reciprocal	98860000.0000
total_estimate	0.6816
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	30.1 Å
skewness	0.324
kurtosis	-0.640
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	27680000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 0.077; Positv: 1.000; Valcen: 0.956; Smooth: 0.939

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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	6897

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	1

Entity 3 non-polymer

description	(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid
formula_weight	389.3 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	896

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6. Citations (1)

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length_a	43.260 Å
length_b	83.724 Å
length_c	207.777 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	1.590 Å
resolution_low	42.350 Å
r_factor	0.1741
r_work	0.1734
r_free	0.2141

fit	/app/data/saxs_computation/s5/9s5m/9s5m.fit
pddf	/app/data/pr_computation/s5/9s5m/9s5m.pr.out
profile	/app/data/saxs_computation/s5/9s5m/9s5m.dat