← Back to search

9xfx

Crystal structure of Class A beta-lactamase BlaA in complex with Tebipenem (imine form)

Method: X-RAY DIFFRACTION D_max: 61.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9xfx
deposition_date	2025-10-29
last_revision	2025-11-12
title	Crystal structure of Class A beta-lactamase BlaA in complex with Tebipenem (imine form)
keywords	Partial Carbapenemase, Acyl enzyme complex, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	18.82 Å
rg_electron	17.81 Å
i0	29324700.00
molecular_weight	27175.0 kDa
excluded_volume	25897 Å³
envelope_volume	40486 Å³
shell_volume	18831 Å³
envelope_diameter	64.3 Å
shell_rg	24.35 Å
envelope_rg	18.20 Å
shape_rg	17.77 Å
total_rg	18.55 Å
total_atoms	2051
n_residues	264
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	61.0 Å
rg_real	18.74 Å
rg_real_error	0.34 Å
i0_real	2.9320e+07
i0_real_error	3.4840e+05
rg_reciprocal	18.76 Å
i0_reciprocal	29320000.0000
total_estimate	0.8059
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.4 Å
skewness	0.279
kurtosis	-0.247
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	6687000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Beta-lactamase
formula_weight	31966.6 kDa
ec_number	3.5.2.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2373

MKHSSLRRSLLLAGITLPLVSFALPAWANALPASVDKQLAELERNANGRLGVAMINTGNGTKILYRAAQRFPFCSTFKFMLAAAVLDQSQSQPNLLNKHINYHESDLLSYAPITRKNLAHGMTVSELCAATIQYSDNTAANLLIKELGGLAAVNQFARSIGDQMFRLDRWEPDLNTARPNDPRDTTTPAAMAASMNKLVLGDALRPAQRSQLAVWLKGNTTGDATIRAGAPTDWIVGDKTGSGDYGTTNDIAVLWPTKGAPIVLVVYFTQREKDAKPRRDVLASVTKIILSQIS

Source

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

Entity 2 non-polymer

description	TEBIPENEM, BOUND FORM
formula_weight	385.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	275

▶

6. Citations (1)

▶

length_a	91.342 Å
length_b	72.182 Å
length_c	43.543 Å
angle_alpha	90.00 °
angle_beta	96.09 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.500 Å
resolution_low	24.597 Å
r_factor	—
r_work	0.1729
r_free	0.2039

fit	/app/data/saxs_computation/xf/9xfx/9xfx.fit
pddf	/app/data/pr_computation/xf/9xfx/9xfx.pr.out
profile	/app/data/saxs_computation/xf/9xfx/9xfx.dat