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9xte

E.coli delta lepA 30S ribosomal subunit class A, body domain

Method: ELECTRON MICROSCOPY D_max: 199.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xte
deposition_date	2025-11-22
title	E.coli delta lepA 30S ribosomal subunit class A, body domain
keywords	30S subunit maturation, LepA, cryo-EM, ribosome assembly, RIBOSOME; RIBOSOME
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	56.83 Å
rg_electron	57.22 Å
i0	7981730000.00
molecular_weight	494330.0 kDa
excluded_volume	511330 Å³
envelope_volume	829610 Å³
shell_volume	120110 Å³
envelope_diameter	213.9 Å
shell_rg	59.58 Å
envelope_rg	56.97 Å
shape_rg	57.22 Å
total_rg	57.27 Å
total_atoms	33281
n_residues	2456
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	199.7 Å
rg_real	56.97 Å
rg_real_error	2.35 Å
i0_real	7.9820e+09
i0_real_error	1.7020e+08
rg_reciprocal	56.71 Å
i0_reciprocal	7979000000.0000
total_estimate	0.7936
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	64.2 Å
skewness	0.453
kurtosis	-0.179
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	394700000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (15)

Entity 1 polymer

description	30S ribosomal protein S4
formula_weight	23514.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D
atom_count	35512

MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK

Entity 2 polymer

description	30S ribosomal protein S5
formula_weight	17629.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Entity 3 polymer

description	30S ribosomal protein S6, fully modified isoform
formula_weight	15727.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANETADDAEAGDSEEEEEE

Entity 4 polymer

description	30S ribosomal protein S8
formula_weight	14146.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA

Entity 5 polymer

description	30S ribosomal protein S12
formula_weight	13814.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA

Entity 6 polymer

description	30S ribosomal protein S15
formula_weight	10290.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	O

MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR

Entity 7 polymer

description	Small ribosomal subunit protein bS16
formula_weight	9136.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKA

Entity 8 polymer

description	30S ribosomal protein S17
formula_weight	9724.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Q

MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAVL

Entity 9 polymer

description	30S ribosomal protein S18
formula_weight	9005.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ

Entity 10 polymer

description	30S ribosomal protein S20
formula_weight	9708.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	T

MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA

Entity 11 polymer

description	RNA (1026-MER)
formula_weight	499705.0 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A

AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 12 polymer

description	30S ribosomal protein S2
formula_weight	26781.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEAE

Entity 13 polymer

description	Small ribosomal subunit protein uS11
formula_weight	13871.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV

Entity 14 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	34

Entity 15 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2231

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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	2.24 Å
resolution_method	—
num_particles	297347

fit	/app/data/saxs_computation/xt/9xte/9xte.fit
pddf	/app/data/pr_computation/xt/9xte/9xte.pr.out
profile	/app/data/saxs_computation/xt/9xte/9xte.dat

E.coli delta lepA 30S ribosomal subunit class A, body domain

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

EM 3D

5. Entities & Polymer Info (15)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Source

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

Entity 14 non-polymer

Entity 15 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)