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9vgv

Crystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole.

Method: X-RAY DIFFRACTION D_max: 61.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vgv
deposition_date	2025-06-15
last_revision	2025-08-06
title	Crystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole.
keywords	Acyl Enzyme complex, beta-lactamase inhibitor, Transition state analogue, Complex crystal structure, 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	18.67 Å
rg_electron	17.70 Å
i0	27602500.00
molecular_weight	26488.0 kDa
excluded_volume	25338 Å³
envelope_volume	40043 Å³
shell_volume	18701 Å³
envelope_diameter	64.2 Å
shell_rg	24.25 Å
envelope_rg	18.09 Å
shape_rg	17.69 Å
total_rg	18.42 Å
total_atoms	2004
n_residues	260
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	61.1 Å
rg_real	18.58 Å
rg_real_error	0.31 Å
i0_real	2.7600e+07
i0_real_error	3.3890e+05
rg_reciprocal	18.60 Å
i0_reciprocal	27600000.0000
total_estimate	0.8841
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.4 Å
skewness	0.253
kurtosis	-0.298
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0001
highest_alpha	6303000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Beta-lactamase
formula_weight	28464.4 kDa
ec_number	3.5.2.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2061

SVDKQLAELERNANGRLGVAMINTGNGTKILYRAAQRFPFCSTFKFMLAAAVLDQSQSQPNLLNKHINYHESDLLSYAPITRKNLAHGMTVSELCAATIQYSDNTAANLLIKELGGLAAVNQFARSIGDQMFRLDRWEPDLNTARPNDPRDTTTPAAMAASMNKLVLGDALRPAQRSQLAVWLKGNTTGDATIRAGAPTDWIVGDKTGSGDYGTTNDIAVLWPTKGAPIVLVVYFTQREKDAKPRRDVLASVTKIILSQIS

Source

organism	Yersinia enterocolitica
ncbi_taxonomy_id	630
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	Tavaborole
formula_weight	151.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	37

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6. Citations (1)

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length_a	91.494 Å
length_b	72.980 Å
length_c	43.938 Å
angle_alpha	90.00 °
angle_beta	94.42 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.500 Å
resolution_low	23.516 Å
r_factor	—
r_work	0.1966
r_free	0.2694

fit	/app/data/saxs_computation/vg/9vgv/9vgv.fit
pddf	/app/data/pr_computation/vg/9vgv/9vgv.pr.out
profile	/app/data/saxs_computation/vg/9vgv/9vgv.dat

Crystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole.

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