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9v4a

Crystal Structure of Xeruborbactam (QPX7728) in complex with SME-1 class A carbapenemase

Method: X-RAY DIFFRACTION D_max: 64.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v4a
deposition_date	2025-05-23
title	Crystal Structure of Xeruborbactam (QPX7728) in complex with SME-1 class A carbapenemase
keywords	Boronic acid, complex, carbapenemase, 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	18.77 Å
rg_electron	17.79 Å
i0	15853100.00
molecular_weight	29645.0 kDa
excluded_volume	36934 Å³
envelope_volume	40500 Å³
shell_volume	18796 Å³
envelope_diameter	64.4 Å
shell_rg	24.37 Å
envelope_rg	18.28 Å
shape_rg	17.78 Å
total_rg	18.75 Å
total_atoms	2083
n_residues	267
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	64.7 Å
rg_real	18.69 Å
rg_real_error	0.48 Å
i0_real	1.5850e+07
i0_real_error	2.3120e+05
rg_reciprocal	18.70 Å
i0_reciprocal	15850000.0000
total_estimate	0.8603
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.0 Å
skewness	0.274
kurtosis	-0.230
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	3927000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.729; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Beta-lactamase SME-1
formula_weight	30403.3 kDa
ec_number	3.5.2.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2119

MGNKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAIDHHHHHH

Source

organism	Serratia marcescens
ncbi_taxonomy_id	615
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	(1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid
formula_weight	222.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	36

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6. Citations (1)

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length_a	36.266 Å
length_b	50.505 Å
length_c	60.484 Å
angle_alpha	90.00 °
angle_beta	98.53 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.400 Å
resolution_low	25.747 Å
r_factor	—
r_work	0.1768
r_free	0.2694

fit	/app/data/saxs_computation/v4/9v4a/9v4a.fit
pddf	/app/data/pr_computation/v4/9v4a/9v4a.pr.out
profile	/app/data/saxs_computation/v4/9v4a/9v4a.dat