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9sge

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (Aztreonam)

Method: X-RAY DIFFRACTION D_max: 87.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sge
deposition_date	2025-08-22
title	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (Aztreonam)
keywords	CELL WALL, PEPTIDOGLYCAN SYNTHESIS ENZYME, DRUG-BINDING PROTEIN, MONOBACTAM, TRANSFERASE; TRANSFERASE
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	24.58 Å
rg_electron	23.85 Å
i0	47305000.00
molecular_weight	50697.0 kDa
excluded_volume	62146 Å³
envelope_volume	74717 Å³
shell_volume	26591 Å³
envelope_diameter	93.5 Å
shell_rg	30.82 Å
envelope_rg	24.56 Å
shape_rg	23.85 Å
total_rg	24.61 Å
total_atoms	3524
n_residues	448
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	87.8 Å
rg_real	24.65 Å
rg_real_error	0.64 Å
i0_real	4.7300e+07
i0_real_error	6.8980e+05
rg_reciprocal	24.64 Å
i0_reciprocal	47300000.0000
total_estimate	0.6695
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.492
kurtosis	0.012
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	8075000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.691; Stabil: 1.000; Sysdev: 0.264; Positv: 1.000; Valcen: 0.891; Smooth: 0.942

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Penicillin-binding protein 1B
formula_weight	54085.9 kDa
mutation	N656G, R686Q, R687Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3962

DISSISEITYSDGTVIASIESDMLRQDFLPSGTVTGISQDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSLP

Source

organism	Streptococcus pneumoniae
ncbi_taxonomy_id	1313
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;2-({[(1Z)-1-(2-amino-1,3-thiazol-4-yl)-2-oxo-2-{[(2S,3S)-1-oxo-3-(sulfoamino)butan-2-yl]amino}ethylidene]amino}oxy)-2-methylpropanoic acid ;
formula_weight	437.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	27

Entity 4 non-polymer

description	2-AMINOETHANESULFONIC ACID
formula_weight	125.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	404

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6. Citations (1)

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length_a	96.306 Å
length_b	147.180 Å
length_c	98.117 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.647 Å
resolution_low	41.904 Å
r_factor	—
r_work	0.1735
r_free	0.1898

fit	/app/data/saxs_computation/sg/9sge/9sge.fit
pddf	/app/data/pr_computation/sg/9sge/9sge.pr.out
profile	/app/data/saxs_computation/sg/9sge/9sge.dat