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9sse

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

Method: X-RAY DIFFRACTION D_max: 86.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sse
deposition_date	2025-09-25
title	PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Ampicillin - 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	24.64 Å
rg_electron	23.92 Å
i0	46787400.00
molecular_weight	50932.0 kDa
excluded_volume	62658 Å³
envelope_volume	75358 Å³
shell_volume	26780 Å³
envelope_diameter	91.6 Å
shell_rg	30.82 Å
envelope_rg	24.62 Å
shape_rg	23.91 Å
total_rg	24.67 Å
total_atoms	3552
n_residues	454
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	86.6 Å
rg_real	24.71 Å
rg_real_error	0.73 Å
i0_real	4.6790e+07
i0_real_error	7.5510e+05
rg_reciprocal	24.70 Å
i0_reciprocal	46790000.0000
total_estimate	0.6207
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	77.0 Å
skewness	0.495
kurtosis	0.016
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	7342000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.716; Stabil: 0.997; Sysdev: 0.338; Positv: 1.000; Valcen: 0.912; Smooth: 0.000

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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	3919

DISSISEITYSDGTVIASIESDMLRQDFLPSGTVTGISQDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTGQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGSLP

Source

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

Entity 2 non-polymer

description	(2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
formula_weight	351.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	22

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	330

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6. Citations (1)

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length_a	96.275 Å
length_b	148.859 Å
length_c	99.386 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	1.790 Å
resolution_low	48.138 Å
r_factor	—
r_work	0.1679
r_free	0.1890

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

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

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