SAXSdb — 9xka

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1. Structure Basics

entry_id	9xka
deposition_date	2025-11-05
title	Cryo-EM structure of Streptococcus thermophilus FoeAB in complex with AMPPNP
keywords	fosfomycin, ABC transporter, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	37.99 Å
rg_electron	38.28 Å
i0	231744000.00
molecular_weight	129300.0 kDa
excluded_volume	164580 Å³
envelope_volume	219370 Å³
shell_volume	49288 Å³
envelope_diameter	129.3 Å
shell_rg	43.20 Å
envelope_rg	37.15 Å
shape_rg	38.27 Å
total_rg	38.65 Å
total_atoms	9098
n_residues	1145
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	130.2 Å
rg_real	38.16 Å
rg_real_error	1.24 Å
i0_real	2.3170e+08
i0_real_error	4.0360e+06
rg_reciprocal	38.06 Å
i0_reciprocal	231700000.0000
total_estimate	0.8731
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.3 Å
skewness	0.445
kurtosis	-0.347
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	32060000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.910

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
formula_weight	67879.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9109

MKALLVYFKGFVKDSILGPVFKLIEASFELLVPMVIAGIVDITIPNRDQNHLFMMIFLLFGLAVIGVVVAISAQYFSSRAAVGYAQALTNDLYAKIMRLSKEKRDEIGTSSLVTRLTGDTFQIQTGINQFLRLFLRAPIIVTGAIIMAFRISPRLTLWFIGMVLVLSLIIVLASRIVNPLYAKIRLINESIVTNTRQQLEGMRVIRAFGQSERELDNFTTVNKELKKWQLKTGVISSLISPLTFLVVNMTLIAILWQGNVQIQGGLLSQGMLIALVNYLLQILAELLKLAMMLTNLNQSFISAKRVQAIFNLQDEDIEAPLIIKKPNQPSIALEIDKMTFTYPTASQPSLQEIDFKTFEGESLGIIGGTGSGKSTLVNLIMNLYKPQFGSLTIFKNQLSPNNLKEWRSWVAYVPQKAELFRGTIRSNLSLGLDYEPSDQELWHALDMAQASDFVREKELGLDEPVESFGRNFSGGQRQRLTIARALMRPAPFLILDDSTSALDYLTESRLLAAIRENLKSTSLIIISQRPNSLKAVDQILVLDKGHQVGLGNHEELLATNKIYQDIHYSQHQKVVADEGGSAWSHPQFEKGGGSGGGSGGSAWSHPQLEK

Source

organism	Streptococcus thermophilus
ncbi_taxonomy_id	1308
host_organism	Escherichia coli B

Entity 2 polymer

description	Lipid/multidrug/protein-type ABC exporter, ATP binding/membrane-spanning protein
formula_weight	65864.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MKARNNKSTLKRLCKDILSQCYLFALATVGTIVQVALTVYFPILLGDAVDAVLKMNAVFLMSRLIWQMLLLILANSAIQWLNPLIYNRLIYSYSESLRERVMMKIHAIPFSYLDRQGTGDMVSRVTTDSDQLNNGLLMFFNQFFVGLLTIFVIIITMARLDWFMMLLVLVMTPLSMLVTRFIARKSYQLYRNQTKWRGKQTQLIEESLTQEALVQILNAQDQMVRNFNEVNGKYANYSQGAIFYSSAVNPATRFFNSLLYALITGVGAYRIMSGGTFTVGQLTTFLNYVTQYTKPFNDISSVLSELQSALACADRLYMILDEDEIPETGNAVLDEAEVQGHFQFDHVQFGYLQNKPLIKDLSIDIPAASTVAIVGPTGAGKSTLINLLMRFYDLDKGQILLDGRDITYYTRESLRKQIGMVLQETWLKVATIHDNIAYGNPKASREEVVAAAKAANADFFIKQLPLGYDTFLKDAGQSLSQGQRQLLTIARIFVNVPKILILDEATSSIDTRTELLIQEAFAKLMKGRTSFIIAHRLSTIENADLILVMNNGDIVEHGTHNQLMRTKGMYYRMQTAQKTQNN

Source

organism	Streptococcus thermophilus
ncbi_taxonomy_id	1308
host_organism	Escherichia coli B

Entity 3 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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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	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	245983

fit	/app/data/saxs_computation/xk/9xka/9xka.fit
pddf	/app/data/pr_computation/xk/9xka/9xka.pr.out
profile	/app/data/saxs_computation/xk/9xka/9xka.dat

Cryo-EM structure of Streptococcus thermophilus FoeAB in complex with AMPPNP

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)