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9u4k

Serine Beta-Lactamase OXA-48 in complex with Dual MBL/SBL inhibitor FB3-4

Method: X-RAY DIFFRACTION D_max: 144.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u4k
deposition_date	2025-03-19
last_revision	2026-03-25
title	Serine Beta-Lactamase OXA-48 in complex with Dual MBL/SBL inhibitor FB3-4
keywords	inhibitor, Complex, HYDROLASE; HYDROLASE
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	44.89 Å
rg_electron	44.30 Å
i0	740491000.00
molecular_weight	226700.0 kDa
excluded_volume	284030 Å³
envelope_volume	388870 Å³
shell_volume	72294 Å³
envelope_diameter	151.4 Å
shell_rg	50.31 Å
envelope_rg	43.13 Å
shape_rg	44.29 Å
total_rg	44.62 Å
total_atoms	31591
n_residues	1928
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	144.6 Å
rg_real	44.71 Å
rg_real_error	1.81 Å
i0_real	7.4050e+08
i0_real_error	1.5770e+07
rg_reciprocal	44.89 Å
i0_reciprocal	740600000.0000
total_estimate	0.8904
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	57.8 Å
skewness	0.164
kurtosis	-0.436
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	70260000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.877

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Beta-lactamase OXA-48
formula_weight	28097.8 kDa
ec_number	3.5.2.6
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	32554

EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP

Source

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	2-[[(3~{R})-6-(2-fluoranylethoxy)-1-oxidanyl-3~{H}-2,1-benzoxaborol-3-yl]methyl]prop-2-enoic acid
formula_weight	280.1 kDa
src_method	syn
entity_count	8

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	963

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6. Citations (1)

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length_a	59.607 Å
length_b	95.751 Å
length_c	108.690 Å
angle_alpha	89.96 °
angle_beta	90.05 °
angle_gamma	107.55 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.178 Å
resolution_low	34.963 Å
r_factor	0.1926
r_work	0.1917
r_free	0.2455

fit	/app/data/saxs_computation/u4/9u4k/9u4k.fit
pddf	/app/data/pr_computation/u4/9u4k/9u4k.pr.out
profile	/app/data/saxs_computation/u4/9u4k/9u4k.dat

Serine Beta-Lactamase OXA-48 in complex with Dual MBL/SBL inhibitor FB3-4

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