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9uj6

Crystal structure of SME-1 E166A in complex with cefsulodin

Method: X-RAY DIFFRACTION D_max: 92.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uj6
deposition_date	2025-04-17
last_revision	2026-04-22
title	Crystal structure of SME-1 E166A in complex with cefsulodin
keywords	Carbapenemase, deacylation deficient mutant, 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	28.19 Å
rg_electron	27.56 Å
i0	59293100.00
molecular_weight	59171.0 kDa
excluded_volume	73636 Å³
envelope_volume	87329 Å³
shell_volume	27262 Å³
envelope_diameter	97.1 Å
shell_rg	33.70 Å
envelope_rg	27.73 Å
shape_rg	27.55 Å
total_rg	28.16 Å
total_atoms	4160
n_residues	533
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	92.3 Å
rg_real	28.36 Å
rg_real_error	0.71 Å
i0_real	5.9290e+07
i0_real_error	9.5260e+05
rg_reciprocal	28.31 Å
i0_reciprocal	59290000.0000
total_estimate	0.8644
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.4 Å
skewness	0.413
kurtosis	-0.543
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	18660000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.847; Smooth: 0.856

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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	30403.3 kDa
ec_number	3.5.2.6
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4349

MGNKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAIDHHHHHH

Source

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

Entity 2 non-polymer

description	1-({(2R)-4-carboxy-2-[(R)-carboxy{[(2R)-2-phenyl-2-sulfoacetyl]amino}methyl]-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium
formula_weight	508.5 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	189

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6. Citations (1)

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length_a	36.268 Å
length_b	51.046 Å
length_c	131.316 Å
angle_alpha	90.00 °
angle_beta	92.78 °
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	22.403 Å
r_factor	—
r_work	0.2001
r_free	0.2680

fit	/app/data/saxs_computation/uj/9uj6/9uj6.fit
pddf	/app/data/pr_computation/uj/9uj6/9uj6.pr.out
profile	/app/data/saxs_computation/uj/9uj6/9uj6.dat

Crystal structure of SME-1 E166A in complex with cefsulodin

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