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9sgb

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (22)

Method: X-RAY DIFFRACTION D_max: 89.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sgb
deposition_date	2025-08-22
title	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (22)
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	24.68 Å
rg_electron	24.16 Å
i0	92691100.00
molecular_weight	49396.0 kDa
excluded_volume	47010 Å³
envelope_volume	78531 Å³
shell_volume	27521 Å³
envelope_diameter	91.7 Å
shell_rg	31.16 Å
envelope_rg	24.80 Å
shape_rg	24.15 Å
total_rg	24.72 Å
total_atoms	3686
n_residues	470
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	89.6 Å
rg_real	24.76 Å
rg_real_error	0.79 Å
i0_real	9.2690e+07
i0_real_error	1.4290e+06
rg_reciprocal	24.75 Å
i0_reciprocal	92690000.0000
total_estimate	0.7552
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.5 Å
skewness	0.506
kurtosis	0.010
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	12060000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.656; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.846; Smooth: 0.000

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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	4197

DISSISEITYSDGTVIASIESDMLRQDFLPSGTVTGISQDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSLP

Source

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

Entity 2 non-polymer

description	;[(2~{S},3~{S})-3-[[2-(2-azanylidene-1,3-thiazolidin-4-yl)-2-[2-[(2-methylpropan-2-yl)oxy]-2-oxidanylidene-ethoxy]imino-ethanoyl]amino]-4-oxidanylidene-butan-2-yl]sulfamic acid ;
formula_weight	465.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	25

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	477

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6. Citations (1)

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length_a	97.473 Å
length_b	148.153 Å
length_c	97.962 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	1.520 Å
resolution_low	48.736 Å
r_factor	—
r_work	0.1830
r_free	0.2010

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