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9uj8

Crystal structure of SME-1 E166A with cefovecin

Method: X-RAY DIFFRACTION D_max: 62.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uj8
deposition_date	2025-04-17
last_revision	2026-04-22
title	Crystal structure of SME-1 E166A with cefovecin
keywords	Acyl enzyme 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	18.60 Å
rg_electron	17.76 Å
i0	29717000.00
molecular_weight	27543.0 kDa
excluded_volume	26315 Å³
envelope_volume	40649 Å³
shell_volume	18875 Å³
envelope_diameter	64.0 Å
shell_rg	24.45 Å
envelope_rg	18.23 Å
shape_rg	17.76 Å
total_rg	18.46 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	62.4 Å
rg_real	18.52 Å
rg_real_error	0.42 Å
i0_real	2.9720e+07
i0_real_error	3.9810e+05
rg_reciprocal	18.53 Å
i0_reciprocal	29720000.0000
total_estimate	0.7956
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.1 Å
skewness	0.284
kurtosis	-0.244
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	7007000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Beta-lactamase SME-1
formula_weight	30345.3 kDa
ec_number	3.5.2.6
mutation	E166A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2169

MGNKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWALELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAIDHHHHHH

Source

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

Entity 2 non-polymer

description	Acylated Cefovecin
formula_weight	457.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	71

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6. Citations (1)

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length_a	36.295 Å
length_b	50.596 Å
length_c	60.340 Å
angle_alpha	90.00 °
angle_beta	98.03 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	21.540 Å
r_factor	—
r_work	0.1764
r_free	0.2546

fit	/app/data/saxs_computation/uj/9uj8/9uj8.fit
pddf	/app/data/pr_computation/uj/9uj8/9uj8.pr.out
profile	/app/data/saxs_computation/uj/9uj8/9uj8.dat

Crystal structure of SME-1 E166A with cefovecin

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