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9sg6

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (10)

Method: X-RAY DIFFRACTION D_max: 87.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sg6
deposition_date	2025-08-22
title	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (10)
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	24.60 Å
rg_electron	24.05 Å
i0	87095900.00
molecular_weight	47833.0 kDa
excluded_volume	45503 Å³
envelope_volume	76424 Å³
shell_volume	27030 Å³
envelope_diameter	91.5 Å
shell_rg	30.97 Å
envelope_rg	24.68 Å
shape_rg	24.04 Å
total_rg	24.62 Å
total_atoms	3566
n_residues	455
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	87.4 Å
rg_real	24.69 Å
rg_real_error	0.86 Å
i0_real	8.7100e+07
i0_real_error	1.4550e+06
rg_reciprocal	24.67 Å
i0_reciprocal	87090000.0000
total_estimate	0.8443
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.8 Å
skewness	0.507
kurtosis	0.017
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	11700000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.703; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.881; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	3959

DISSISEITYSDGTVIASIESDMLRQDFLPSGTVTGISQDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSLP

Source

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

Entity 2 non-polymer

description	{(2S,3S)-3-[2-(4-nitrophenyl)acetamido]-4-oxobutan-2-yl}sulfamic acid
formula_weight	345.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	28

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	329

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6. Citations (1)

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length_a	96.483 Å
length_b	149.563 Å
length_c	99.467 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	1.740 Å
resolution_low	44.291 Å
r_factor	—
r_work	0.1754
r_free	0.2015

fit	/app/data/saxs_computation/sg/9sg6/9sg6.fit
pddf	/app/data/pr_computation/sg/9sg6/9sg6.pr.out
profile	/app/data/saxs_computation/sg/9sg6/9sg6.dat

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (10)

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