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9teb

Crystal structure of Nocardia cyriacigeorgica, class A beta-lactamase, NCY-1 bound to Avibactam

Method: X-RAY DIFFRACTION D_max: 58.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9teb
deposition_date	2025-11-25
title	Crystal structure of Nocardia cyriacigeorgica, class A beta-lactamase, NCY-1 bound to Avibactam
keywords	beta-lactamase, avibactam, Nocardia, 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	18.52 Å
rg_electron	17.37 Å
i0	14926800.00
molecular_weight	27972.0 kDa
excluded_volume	34503 Å³
envelope_volume	38121 Å³
shell_volume	18158 Å³
envelope_diameter	60.6 Å
shell_rg	23.82 Å
envelope_rg	17.71 Å
shape_rg	17.38 Å
total_rg	18.23 Å
total_atoms	3868
n_residues	259
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	58.9 Å
rg_real	18.42 Å
rg_real_error	0.32 Å
i0_real	1.4930e+07
i0_real_error	1.8680e+05
rg_reciprocal	18.44 Å
i0_reciprocal	14930000.0000
total_estimate	0.8128
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.4 Å
skewness	0.196
kurtosis	-0.344
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	3413000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Beta-lactamase
formula_weight	27942.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4202

GSAVADPRFAALETTAGARLGVFAVNTGSERTVAHRADERFPMASTFKGLACGALLREHPLSTGYFDQVIHYSAEELVDYSPVTETRVESGMTVAELCHAAITASDNTAGNQLLKLLGGPQGFTAFLRSLGDDTSRLDRWETELNTAIPGDERDTTTPAALAADYRALVVGDVLGEPERAQLTAWLVANTTGDTRIRAGLPEDWTVGDKTGSPAYGSALDVAVTWPSGRAPIVIAVLSTKSEQDAEPDNRLVADATRTVVDVLG

Source

organism	Nocardia cyriacigeorgica
ncbi_taxonomy_id	135487
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
formula_weight	267.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	221

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6. Citations (2)

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length_a	54.590 Å
length_b	54.590 Å
length_c	133.210 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	1.300 Å
resolution_low	44.550 Å
r_factor	0.1570
r_work	0.1561
r_free	0.1752

fit	/app/data/saxs_computation/te/9teb/9teb.fit
pddf	/app/data/pr_computation/te/9teb/9teb.pr.out
profile	/app/data/saxs_computation/te/9teb/9teb.dat

Crystal structure of Nocardia cyriacigeorgica, class A beta-lactamase, NCY-1 bound to Avibactam

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