← Back to search

9pzg

;Bacterial ribosomal 2'-O-methyltransferase RsmI in complex with the small ribosomal subunit ;

Method: ELECTRON MICROSCOPY D_max: 215.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9pzg
deposition_date	2025-08-11
last_revision	2025-09-24
title	;Bacterial ribosomal 2'-O-methyltransferase RsmI in complex with the small ribosomal subunit ;
keywords	Ribosome, methylation, 30S subunit, helix 44, methyltransferase; RIBOSOME
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	68.36 Å
rg_electron	68.50 Å
i0	20207700000.00
molecular_weight	820550.0 kDa
excluded_volume	867760 Å³
envelope_volume	1453900 Å³
shell_volume	174160 Å³
envelope_diameter	244.1 Å
shell_rg	70.57 Å
envelope_rg	67.56 Å
shape_rg	68.48 Å
total_rg	68.56 Å
total_atoms	55491
n_residues	4396
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	215.3 Å
rg_real	68.39 Å
rg_real_error	1.43 Å
i0_real	2.0200e+10
i0_real_error	4.2500e+08
rg_reciprocal	67.92 Å
i0_reciprocal	20190000000.0000
total_estimate	0.6217
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	74.9 Å
skewness	0.447
kurtosis	-0.228
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0025
highest_alpha	1243000000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.996; Smooth: 0.182

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (25)

Entity 1 polymer

description	16S rRNA
formula_weight	499760.2 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	55661

AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA

Entity 2 polymer

description	Small ribosomal subunit protein uS2
formula_weight	26781.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEAE

Entity 3 polymer

description	Small ribosomal subunit protein uS3
formula_weight	26031.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Entity 4 polymer

description	Small ribosomal subunit protein uS4
formula_weight	23514.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK

Entity 5 polymer

description	Small ribosomal subunit protein uS5
formula_weight	17629.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK

Entity 6 polymer

description	Small ribosomal subunit protein bS6, fully modified isoform
formula_weight	15727.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANETADDAEAGDSEEEEEE

Entity 7 polymer

description	Small ribosomal subunit protein uS7
formula_weight	20055.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEAFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Entity 8 polymer

description	Small ribosomal subunit protein uS8
formula_weight	14146.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MSMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPELELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGEIICYVA

Entity 9 polymer

description	Small ribosomal subunit protein uS9
formula_weight	14886.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR

Entity 10 polymer

description	Small ribosomal subunit protein uS10
formula_weight	11755.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Entity 11 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 12 polymer

description	Small ribosomal subunit protein uS12
formula_weight	13768.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA

Entity 13 polymer

description	Small ribosomal subunit protein uS13
formula_weight	13128.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK

Entity 14 polymer

description	Small ribosomal subunit protein uS14
formula_weight	11606.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW

Entity 15 polymer

description	Small ribosomal subunit protein uS15
formula_weight	10290.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	O

MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR

Entity 16 polymer

description	Small ribosomal subunit protein bS16
formula_weight	9207.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA

Entity 17 polymer

description	Small ribosomal subunit protein uS17
formula_weight	9724.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Q

MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAVL

Entity 18 polymer

description	Small ribosomal subunit protein bS18
formula_weight	9005.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ

Entity 19 polymer

description	Small ribosomal subunit protein uS19
formula_weight	10455.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTYRGHAADKKAKKK

Entity 20 polymer

description	Small ribosomal subunit protein bS20
formula_weight	9708.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	T

MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA

Entity 21 polymer

description	Small ribosomal subunit protein bS21
formula_weight	8524.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	U

MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY

Entity 22 polymer

description	Ribosomal RNA small subunit methyltransferase I
formula_weight	33313.0 kDa
ec_number	2.1.1.198
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	V,W

MHHHHHHASGLVPRGSHMKQHQSADNSQGQLYIVPTPIGNLADITQRALEVLQAVDLIAAEDTRHTGLLLQHFGINARLFALHDHNEQQKAETLLAKLQEGQNIALVSDAGTPLINDPGYHLVRTCREAGIRVVPLPGPCAAITALSAAGLPSDRFCYEGFLPAKSKGRRDALKAIEAEPRTLIFYESTHRLLDSLEDIVAVLGESRYVVLARELTKTWETIHGAPVGELLAWVKEDENRRKGEMVLIVEGHKAQEEDLPADALRTLALLQAELPLKKAAALAAEIHGVKKNALYKYALEQQG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 23 non-polymer

description	5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
formula_weight	395.4 kDa
src_method	nat
entity_count	2

Entity 24 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	79

Entity 25 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	170

▶

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	2.42 Å
resolution_method	—
num_particles	74553

fit	/app/data/saxs_computation/pz/9pzg/9pzg.fit
pddf	/app/data/pr_computation/pz/9pzg/9pzg.pr.out
profile	/app/data/saxs_computation/pz/9pzg/9pzg.dat

;Bacterial ribosomal 2'-O-methyltransferase RsmI in complex with the small ribosomal subunit ;

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 (25)

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 polymer

Polymer

Entity 15 polymer

Polymer

Entity 16 polymer

Polymer

Entity 17 polymer

Polymer

Entity 18 polymer

Polymer

Entity 19 polymer

Polymer

Entity 20 polymer

Polymer

Entity 21 polymer

Polymer

Entity 22 polymer

Polymer

Source

Entity 23 non-polymer

Entity 24 non-polymer

Entity 25 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)