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9ssg

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Cephalexin - Streptococcus pneumoniae R6

Method: X-RAY DIFFRACTION D_max: 88.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ssg
deposition_date	2025-09-25
title	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Cephalexin - Streptococcus pneumoniae R6
keywords	CELL WALL, PEPTIDOGLYCAN SYNTHESIS ENZYME, INFECTION, DRUG-BINDING PROTEIN, ANTIBIOTICS, 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	24.44 Å
rg_electron	23.90 Å
i0	87229900.00
molecular_weight	47935.0 kDa
excluded_volume	45609 Å³
envelope_volume	75200 Å³
shell_volume	26742 Å³
envelope_diameter	91.3 Å
shell_rg	30.85 Å
envelope_rg	24.65 Å
shape_rg	23.90 Å
total_rg	24.46 Å
total_atoms	3571
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	88.0 Å
rg_real	24.53 Å
rg_real_error	0.91 Å
i0_real	8.7230e+07
i0_real_error	1.3470e+06
rg_reciprocal	24.51 Å
i0_reciprocal	87230000.0000
total_estimate	0.8359
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.515
kurtosis	0.043
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	11440000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.675; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.855; Smooth: 0.982

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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	4123

DISSISEITYSDGTVIASIESDMLRQDFLPSGTVTGISQDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSLP

Source

organism	Streptococcus pneumoniae R6
ncbi_taxonomy_id	171101
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;(2~{R})-2-[(1~{R})-1-[[(2~{R})-2-azanyl-2-phenyl-ethanoyl]amino]-2-oxidanylidene-ethyl]-5-methyl-5,6-dihydro-2~{H}-1,3-thiazine-4-carboxylic acid ;
formula_weight	349.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	29

Entity 4 non-polymer

description	SULFITE ION
formula_weight	80.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	532

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6. Citations (1)

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length_a	96.049 Å
length_b	148.162 Å
length_c	99.185 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	1.642 Å
resolution_low	48.025 Å
r_factor	—
r_work	0.1708
r_free	0.1953

fit	/app/data/saxs_computation/ss/9ssg/9ssg.fit
pddf	/app/data/pr_computation/ss/9ssg/9ssg.pr.out
profile	/app/data/saxs_computation/ss/9ssg/9ssg.dat