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9uj7

Crystal Structure of SME-1 E166A in complex with cefoperazone

Method: X-RAY DIFFRACTION D_max: 88.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uj7
deposition_date	2025-04-17
last_revision	2026-04-22
title	Crystal Structure of SME-1 E166A in complex with cefoperazone
keywords	Carbapenemase, acyl-enzyme 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	26.17 Å
rg_electron	25.65 Å
i0	115357000.00
molecular_weight	55639.0 kDa
excluded_volume	53158 Å³
envelope_volume	87535 Å³
shell_volume	28787 Å³
envelope_diameter	90.8 Å
shell_rg	32.67 Å
envelope_rg	25.77 Å
shape_rg	25.65 Å
total_rg	26.16 Å
total_atoms	4201
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

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3. P(r) Analysis (GNOM)

dmax	88.0 Å
rg_real	26.21 Å
rg_real_error	0.74 Å
i0_real	1.1540e+08
i0_real_error	1.7150e+06
rg_reciprocal	26.20 Å
i0_reciprocal	115400000.0000
total_estimate	0.8767
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.9 Å
skewness	0.400
kurtosis	-0.350
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	25970000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.949

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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	30345.3 kDa
ec_number	3.5.2.6
mutation	E166A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	4313

MGNKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWALELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAIDHHHHHH

Source

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

Entity 2 non-polymer

description	Hydrolysed Cefoperazone
formula_weight	533.6 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	6

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	112

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6. Citations (1)

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length_a	71.594 Å
length_b	51.352 Å
length_c	77.997 Å
angle_alpha	90.00 °
angle_beta	114.05 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.200 Å
resolution_low	23.183 Å
r_factor	—
r_work	0.1622
r_free	0.2466

fit	/app/data/saxs_computation/uj/9uj7/9uj7.fit
pddf	/app/data/pr_computation/uj/9uj7/9uj7.pr.out
profile	/app/data/saxs_computation/uj/9uj7/9uj7.dat