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9s4f

Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 right tail

Method: ELECTRON MICROSCOPY D_max: 111.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s4f
deposition_date	2025-07-28
title	Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 right tail
keywords	Iron acquisition, Hemophore, Hemoglobin, NEAT domain, METAL TRANSPORT; METAL TRANSPORT
method	ELECTRON MICROSCOPY

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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	32.22 Å
rg_electron	31.99 Å
i0	76031000.00
molecular_weight	70843.0 kDa
excluded_volume	89314 Å³
envelope_volume	119210 Å³
shell_volume	33156 Å³
envelope_diameter	118.0 Å
shell_rg	36.40 Å
envelope_rg	32.06 Å
shape_rg	31.99 Å
total_rg	32.40 Å
total_atoms	5012
n_residues	619
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	111.0 Å
rg_real	32.55 Å
rg_real_error	1.29 Å
i0_real	7.6030e+07
i0_real_error	1.2280e+06
rg_reciprocal	32.41 Å
i0_reciprocal	76020000.0000
total_estimate	0.8353
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.7 Å
skewness	0.584
kurtosis	-0.149
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	16590000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.739; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.846; Smooth: 0.801

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Hemoglobin subunit alpha
formula_weight	15051.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5012

LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

Entity 2 polymer

description	Hemoglobin subunit beta
formula_weight	15791.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

HLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

Entity 3 polymer

description	Iron-regulated surface determinant protein H
formula_weight	41500.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MADESLQDAIKNPAIIDKEHTADNWRPIDFQMKNDKGERQFYHYASTVEPATVIFTKTGPIIELGLKTASTWKKFEVYEGDKKLPVELVSYDSDKDYAYIRFPVSNGTREVKIVSSIEYGENIHEDYDYTLMVFAQPITNNPDDYVDEETYNLQKLLAPYHKAKTLERQVYELEKLQEKLPEKYKAEYKKKLDQTRVELADQVKSAVTEFENVTPTNDQLTDVQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDINTKDDDTSQNENLYFQSAWSHPQFEK

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 4 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	4.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.20 Å
resolution_method	—
num_particles	8400

fit	/app/data/saxs_computation/s4/9s4f/9s4f.fit
pddf	/app/data/pr_computation/s4/9s4f/9s4f.pr.out
profile	/app/data/saxs_computation/s4/9s4f/9s4f.dat

Human carboxyhemoglobin bound to Staphylococcus aureus IsdH-N2N3 - 2IsdH:Hbdim complex - 3DVA component 4 right tail

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

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)