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9ulp

Crystal structure of FtsB from Streptococcus pyogenes in complex with Nb1 nanobody

Method: X-RAY DIFFRACTION D_max: 115.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ulp
deposition_date	2025-04-20
last_revision	2026-03-25
title	Crystal structure of FtsB from Streptococcus pyogenes in complex with Nb1 nanobody
keywords	VHH, FtsB, iron acquisition, siderophore, anti-bacterial strategy, IMMUNE SYSTEM; IMMUNE SYSTEM
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	34.08 Å
rg_electron	34.16 Å
i0	109545000.00
molecular_weight	87026.0 kDa
excluded_volume	110310 Å³
envelope_volume	141260 Å³
shell_volume	35518 Å³
envelope_diameter	118.5 Å
shell_rg	39.67 Å
envelope_rg	33.46 Å
shape_rg	34.11 Å
total_rg	34.73 Å
total_atoms	6146
n_residues	784
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	115.5 Å
rg_real	34.22 Å
rg_real_error	0.88 Å
i0_real	1.0950e+08
i0_real_error	1.6370e+06
rg_reciprocal	34.14 Å
i0_reciprocal	109500000.0000
total_estimate	0.8728
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.2 Å
skewness	0.422
kurtosis	-0.422
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	22430000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.919; Smooth: 0.857

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Iron-hydroxamate ABC transporter substrate-binding protein
formula_weight	31849.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6236

SNTASKSLSPMPQIAGVTYYGDIPKQPKRVVSLASTYTGYLKKLDMNLVGVTSYDKKNPILAKTVKKAKQVAATDLEAITTLKPDLIVVGSTEENIKQLAEIAPVISIEYRKRDYLQVLSDFGRIFNKEGKAKKWLKDWKTKTAAYEKEVKAVTGDKATFTIMGLYEKDVYLFGKDWGRGGEIIHQAFHYDAPEKVKTEVFKQGYLSLSQEVLPDYIGDYVVIAAEDDKTGSALYESKLWQSIPAVKKHHVIKVNANVFYFTDPLSLEYQLETLREAILSSEN

Source

organism	Streptococcus pyogenes
ncbi_taxonomy_id	1314
host_organism	Escherichia coli

Entity 2 polymer

description	VHH
formula_weight	13512.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

QVQLVESGGGLVQPGGSLRLSCAASRSIIGINVAGWYRQAPGKQRELVAVITTGGSTNYADSAKGRFTISRDNAQNTLYLQMNSLKPSDTAVYYCNVRGHPPLTYDYWGQGTRVTVSSHHHHHH

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	81

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6. Citations (1)

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length_a	38.364 Å
length_b	60.464 Å
length_c	318.084 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.550 Å
resolution_low	48.180 Å
r_factor	0.2557
r_work	0.2531
r_free	0.3066

fit	/app/data/saxs_computation/ul/9ulp/9ulp.fit
pddf	/app/data/pr_computation/ul/9ulp/9ulp.pr.out
profile	/app/data/saxs_computation/ul/9ulp/9ulp.dat

Crystal structure of FtsB from Streptococcus pyogenes in complex with Nb1 nanobody

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

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)