← Back to search

9xtc

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

Method: ELECTRON MICROSCOPY D_max: 198.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9xtc
deposition_date	2025-11-22
title	E.coli delta lepA 30S ribosomal subunit class C, body domain
keywords	30S subunit maturationk, 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	57.13 Å
rg_electron	57.42 Å
i0	9938720000.00
molecular_weight	544780.0 kDa
excluded_volume	558830 Å³
envelope_volume	909490 Å³
shell_volume	130170 Å³
envelope_diameter	217.1 Å
shell_rg	60.84 Å
envelope_rg	57.02 Å
shape_rg	57.42 Å
total_rg	57.49 Å
total_atoms	36614
n_residues	2613
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	198.6 Å
rg_real	57.24 Å
rg_real_error	2.01 Å
i0_real	9.9390e+09
i0_real_error	1.8640e+08
rg_reciprocal	57.03 Å
i0_reciprocal	9935000000.0000
total_estimate	0.7928
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	63.8 Å
skewness	0.462
kurtosis	-0.138
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	784200000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (15)

Entity 1 polymer

description	RNA (1176-MER)
formula_weight	499817.3 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	39857

AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Entity 2 polymer

description	Small ribosomal subunit protein bS6, non-modified isoform
formula_weight	11669.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEAS

Entity 3 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 4 polymer

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

Polymer

type	polypeptide(L)
strand_id	D

MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK

Entity 5 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 6 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 7 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 8 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 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	30S ribosomal protein S17
formula_weight	9724.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Q

MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAVL

Entity 11 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 12 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 13 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 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	3243

▶

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	2.10 Å
resolution_method	—
num_particles	771814

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

E.coli delta lepA 30S ribosomal subunit class C, 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)