← Back to search

9ujc

Crystal Structure of SME-1 E166A with cefpirome

Method: X-RAY DIFFRACTION D_max: 63.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9ujc
deposition_date	2025-04-17
last_revision	2026-04-22
title	Crystal Structure of SME-1 E166A with cefpirome
keywords	Acyl Enzyme Complex, Carbapenemase, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	18.77 Å
rg_electron	17.78 Å
i0	16303000.00
molecular_weight	29774.0 kDa
excluded_volume	36975 Å³
envelope_volume	40730 Å³
shell_volume	18893 Å³
envelope_diameter	63.8 Å
shell_rg	24.48 Å
envelope_rg	18.24 Å
shape_rg	17.76 Å
total_rg	18.76 Å
total_atoms	4163
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

▼

3. P(r) Analysis (GNOM)

dmax	63.2 Å
rg_real	18.69 Å
rg_real_error	0.40 Å
i0_real	1.6300e+07
i0_real_error	2.1240e+05
rg_reciprocal	18.70 Å
i0_reciprocal	16300000.0000
total_estimate	0.8683
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.258
kurtosis	-0.249
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	4225000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.989

▶

4. Crystallography & Experiment

▶

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	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4278

MGNKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWALELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAIDHHHHHH

Source

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

Entity 2 non-polymer

description	;CEFOTAXIME, C3' cleaved, open, bound form ;
formula_weight	397.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	98

▶

6. Citations (1)

▶

length_a	36.516 Å
length_b	49.888 Å
length_c	61.153 Å
angle_alpha	90.00 °
angle_beta	99.30 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.000 Å
resolution_low	25.820 Å
r_factor	—
r_work	0.1558
r_free	0.2195

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