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9sgd

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (26)

Method: X-RAY DIFFRACTION D_max: 93.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sgd
deposition_date	2025-08-22
title	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (26)
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	24.71 Å
rg_electron	24.19 Å
i0	93617900.00
molecular_weight	49511.0 kDa
excluded_volume	47052 Å³
envelope_volume	78590 Å³
shell_volume	27528 Å³
envelope_diameter	90.9 Å
shell_rg	31.17 Å
envelope_rg	24.82 Å
shape_rg	24.18 Å
total_rg	24.75 Å
total_atoms	3689
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	93.0 Å
rg_real	24.79 Å
rg_real_error	1.00 Å
i0_real	9.3620e+07
i0_real_error	1.5350e+06
rg_reciprocal	24.77 Å
i0_reciprocal	93620000.0000
total_estimate	0.7260
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	26.6 Å
skewness	0.508
kurtosis	0.007
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	12670000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.562; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.773; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

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	4097

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-azanyl-1,3-thiazol-4-yl)-2-(2-methoxy-2-oxidanylidene-ethoxy)imino-ethanoyl]amino]-4-oxidanylidene-butan-2-yl]sulfamic acid ;
formula_weight	423.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SULFITE ION
formula_weight	80.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	27

Entity 5 non-polymer

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

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	376

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6. Citations (1)

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length_a	97.239 Å
length_b	148.297 Å
length_c	98.144 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	1.571 Å
resolution_low	43.567 Å
r_factor	—
r_work	0.1767
r_free	0.2052

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