← Back to search

9xtd

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

Method: ELECTRON MICROSCOPY D_max: 198.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9xtd
deposition_date	2025-11-22
title	E.coli delta lepA 30S ribosomal subunit class B, body domain
keywords	30S subunit maturation, LepA, cryo-EM, ribosome assembly, RIBOSOME; RIBOSOME
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	57.02 Å
rg_electron	57.44 Å
i0	9323730000.00
molecular_weight	529970.0 kDa
excluded_volume	545210 Å³
envelope_volume	895580 Å³
shell_volume	128420 Å³
envelope_diameter	214.3 Å
shell_rg	60.85 Å
envelope_rg	56.90 Å
shape_rg	57.45 Å
total_rg	57.49 Å
total_atoms	35638
n_residues	2574
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

▼

3. P(r) Analysis (GNOM)

dmax	198.2 Å
rg_real	57.11 Å
rg_real_error	1.93 Å
i0_real	9.3240e+09
i0_real_error	1.8680e+08
rg_reciprocal	56.94 Å
i0_reciprocal	9321000000.0000
total_estimate	0.8551
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.7 Å
skewness	0.444
kurtosis	-0.153
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	633900000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.787

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (15)

Entity 1 polymer

description	RNA (1128-MER)
formula_weight	499775.2 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	37507

AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Entity 2 polymer

description	Small ribosomal subunit protein uS4
formula_weight	23383.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

ARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK

Entity 3 polymer

description	Small ribosomal subunit protein uS5
formula_weight	16532.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

ELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILG

Entity 4 polymer

description	Small ribosomal subunit protein bS6, non-modified isoform
formula_weight	12326.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAK

Entity 5 polymer

description	Small ribosomal subunit protein uS8
formula_weight	14015.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

SMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA

Entity 6 polymer

description	Small ribosomal subunit protein uS11
formula_weight	12487.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV

Entity 7 polymer

description	Small ribosomal subunit protein uS12
formula_weight	13683.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA

Entity 8 polymer

description	Small ribosomal subunit protein uS15
formula_weight	10159.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	O

SLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR

Entity 9 polymer

description	30S ribosomal protein S16
formula_weight	9207.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA

Entity 10 polymer

description	Small ribosomal subunit protein uS17
formula_weight	9263.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Q

KIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAV

Entity 11 polymer

description	Small ribosomal subunit protein bS18
formula_weight	6466.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

EIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRH

Entity 12 polymer

description	Small ribosomal subunit protein bS20
formula_weight	9577.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	T

ANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA

Entity 13 polymer

description	Small ribosomal subunit protein uS2
formula_weight	24971.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

VSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQ

Entity 14 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	39

Entity 15 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1869

▶

6. Citations (1)

▶

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	2.26 Å
resolution_method	—
num_particles	269839

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

E.coli delta lepA 30S ribosomal subunit class B, 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

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)