← Back to search

9w7n

Crystal Structure of Vaborbactam in complex with SME-1 class A Carbapenemase

Method: X-RAY DIFFRACTION D_max: 91.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9w7n
deposition_date	2025-08-06
title	Crystal Structure of Vaborbactam in complex with SME-1 class A Carbapenemase
keywords	Boronic acid, Transition state analogue, Inhibitor, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	28.21 Å
rg_electron	27.62 Å
i0	59601700.00
molecular_weight	59644.0 kDa
excluded_volume	74385 Å³
envelope_volume	87517 Å³
shell_volume	27301 Å³
envelope_diameter	95.8 Å
shell_rg	33.65 Å
envelope_rg	27.76 Å
shape_rg	27.60 Å
total_rg	28.25 Å
total_atoms	4193
n_residues	534
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	91.7 Å
rg_real	28.38 Å
rg_real_error	0.81 Å
i0_real	5.9600e+07
i0_real_error	9.4800e+05
rg_reciprocal	28.33 Å
i0_reciprocal	59600000.0000
total_estimate	0.8665
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.419
kurtosis	-0.526
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	18950000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.826

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Beta-lactamase SME-1
formula_weight	29386.2 kDa
ec_number	3.5.2.6
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4486

NKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID

Source

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

Entity 2 non-polymer

description	Vaborbactam
formula_weight	297.1 kDa
src_method	nat
entity_count	2

Entity 3 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	nat
entity_count	2

Entity 4 non-polymer

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

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	237

▶

6. Citations (1)

▶

length_a	36.039 Å
length_b	51.011 Å
length_c	130.533 Å
angle_alpha	90.00 °
angle_beta	92.80 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	23.764 Å
r_factor	—
r_work	0.1849
r_free	0.2418

fit	/app/data/saxs_computation/w7/9w7n/9w7n.fit
pddf	/app/data/pr_computation/w7/9w7n/9w7n.pr.out
profile	/app/data/saxs_computation/w7/9w7n/9w7n.dat