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9w7o

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

Method: X-RAY DIFFRACTION D_max: 86.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w7o
deposition_date	2025-08-06
title	Crystal Structure of Taniborbactam in complex with SME-1 class A Carbapenemase
keywords	Boronic acid based transition state analogue (Batsa), 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	26.82 Å
rg_electron	26.15 Å
i0	59617100.00
molecular_weight	59722.0 kDa
excluded_volume	74588 Å³
envelope_volume	88643 Å³
shell_volume	28534 Å³
envelope_diameter	89.7 Å
shell_rg	33.21 Å
envelope_rg	26.14 Å
shape_rg	26.14 Å
total_rg	26.94 Å
total_atoms	4202
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	86.5 Å
rg_real	26.85 Å
rg_real_error	0.60 Å
i0_real	5.9620e+07
i0_real_error	9.1130e+05
rg_reciprocal	26.84 Å
i0_reciprocal	59620000.0000
total_estimate	0.8957
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	85.0 Å
skewness	0.349
kurtosis	-0.471
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	19500000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.962

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	4621

NKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID

Source

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

Entity 2 non-polymer

description	(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid
formula_weight	389.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	349

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6. Citations (1)

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length_a	70.817 Å
length_b	51.512 Å
length_c	74.697 Å
angle_alpha	90.00 °
angle_beta	113.08 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.930 Å
resolution_low	24.887 Å
r_factor	—
r_work	0.1842
r_free	0.2384

fit	/app/data/saxs_computation/w7/9w7o/9w7o.fit
pddf	/app/data/pr_computation/w7/9w7o/9w7o.pr.out
profile	/app/data/saxs_computation/w7/9w7o/9w7o.dat

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

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