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9xfy

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

Method: X-RAY DIFFRACTION D_max: 60.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xfy
deposition_date	2025-10-29
last_revision	2025-11-12
title	Crystal structure of Class A beta-lactamase BlaA in complex with ertapenem (imine form)
keywords	Imine tautomer, 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	18.85 Å
rg_electron	17.68 Å
i0	15875000.00
molecular_weight	29264.0 kDa
excluded_volume	36336 Å³
envelope_volume	40299 Å³
shell_volume	18810 Å³
envelope_diameter	61.6 Å
shell_rg	24.23 Å
envelope_rg	18.10 Å
shape_rg	17.68 Å
total_rg	18.59 Å
total_atoms	2052
n_residues	262
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	60.7 Å
rg_real	18.76 Å
rg_real_error	0.33 Å
i0_real	1.5870e+07
i0_real_error	1.8480e+05
rg_reciprocal	18.77 Å
i0_reciprocal	15880000.0000
total_estimate	0.8874
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.4 Å
skewness	0.229
kurtosis	-0.276
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	3899000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; 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	31966.6 kDa
ec_number	3.5.2.6
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2264

MKHSSLRRSLLLAGITLPLVSFALPAWANALPASVDKQLAELERNANGRLGVAMINTGNGTKILYRAAQRFPFCSTFKFMLAAAVLDQSQSQPNLLNKHINYHESDLLSYAPITRKNLAHGMTVSELCAATIQYSDNTAANLLIKELGGLAAVNQFARSIGDQMFRLDRWEPDLNTARPNDPRDTTTPAAMAASMNKLVLGDALRPAQRSQLAVWLKGNTTGDATIRAGAPTDWIVGDKTGSGDYGTTNDIAVLWPTKGAPIVLVVYFTQREKDAKPRRDVLASVTKIILSQIS

Source

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

Entity 2 non-polymer

description	;(2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid ;
formula_weight	477.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	212

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6. Citations (1)

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length_a	91.743 Å
length_b	72.818 Å
length_c	43.700 Å
angle_alpha	90.00 °
angle_beta	95.78 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.700 Å
resolution_low	24.663 Å
r_factor	—
r_work	0.1936
r_free	0.2298

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

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

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