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9zcd

Flavobacterium johnsoniae 30S ribosomal subunit.

Method: ELECTRON MICROSCOPY D_max: 239.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zcd
deposition_date	2025-11-23
title	Flavobacterium johnsoniae 30S ribosomal subunit.
keywords	Ribosome, 30S; 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	66.52 Å
rg_electron	67.06 Å
i0	16988300000.00
molecular_weight	738950.0 kDa
excluded_volume	773460 Å³
envelope_volume	1324300 Å³
shell_volume	162820 Å³
envelope_diameter	231.4 Å
shell_rg	68.11 Å
envelope_rg	65.88 Å
shape_rg	67.05 Å
total_rg	67.07 Å
total_atoms	49917
n_residues	3902
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	239.6 Å
rg_real	66.70 Å
rg_real_error	2.53 Å
i0_real	1.6990e+10
i0_real_error	3.5290e+08
rg_reciprocal	66.32 Å
i0_reciprocal	16980000000.0000
total_estimate	0.8465
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	69.9 Å
skewness	0.408
kurtosis	-0.326
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0001
highest_alpha	1724000000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.756

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4. Crystallography & Experiment

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5. Entities & Polymer Info (22)

Entity 1 polymer

description	30S ribosomal protein S1
formula_weight	66159.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	49917

MSEQTKSQEEFLANFNWHNFQEGIDAVDEKNLQEFEELVSKTFIATDQEEVVEGVVVRITDRDVIVDINAKSEGVISLNEFRYNPNLKVGDKVEVLIDIREDKTGQLVLSHRKARTIKSWDRVIAANETGEIVNGFVKCRTKGGMIVDVFGIEAFLPGSQIDVKPIRDYDVYVNKMMEFKVVKINHEFKNVVVSHKALIEADIEVQKKEIIGQLQKGQVLEGVVKNITSYGVFIDLGGVDGLIHITDLSWSRINHPSEVLELDQKLNVVILDFDDEKTRIQLGLKQLNAHPWDALDANLTVGDKVKGKVVVIADYGAFIEVAEGVEGLIHVSEMSWSTHLRSAQDFVKVGDVVEAVILTLDREDRKMSLGIKQLTQDPWTDITSKYPVGSKHTGIVRNFTNFGIFVELEEGIDGLIYISDLSWTKKIKHPSEFVNVGEKLDVVVLELDVEGRKLSLGHKQTTANPWDQYEDSFAVGTIHNGEISEIVDKGATVEFGDDIVAFIPTRHLEKEDGKKLKKGDTADFKVIEFNKEFKRVVASHTAIFREEEEKNVKAAAETTASASTNAPAATLGDNNDVLAALKAKMEKTEKK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 2 polymer

description	30S ribosomal protein S2
formula_weight	28107.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MANKIEVKELLEAGVHFGHMTRKWDPNMAPYIYMERNGIHIINLYKTAAKIEEANEALKKIAASGRKILFVATKKQAKDIVADKAKAANMPYITERWPGGMLTNFVTIRKAVKKMSSIDKMKKDGTFNTLSKKERLQVDRLRAKLEKNLGSIADMSRLPAALFVVDIKAEHIAIKEAQKLNIPVFAMVDTNSDPREVDYVIPANDDASKSIDKILSLVTTAVIEGLSDRGAEKEVEAAEEAPAAEAEAAPATEE

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 3 polymer

description	30S ribosomal protein S3
formula_weight	27886.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	h

MGQKTNPIGNRLGIIRGWDSNWYGGNDYGDKLAEDHKIRKYIHARLSKASVSKVIIERTLKLVTVTITTARPGIIIGKGGQEVDKLKEELKKVTDKEVQINIFEIKRPELDAYLVATSIARQIESRISYRRAIKMAIAASMRMNAEGIKVLISGRLNGAEMARSEGFKEGRIPLSTFRADIDYALAEAHTTYGRMGIKVWIMKGEVYGKRDLSPLAGMDKKQSGTGGGKGGDAPRGKSNFNKGGKPDARKRK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 4 polymer

description	30S ribosomal protein S4
formula_weight	22950.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	i

MARYTGPKTKIARKFGEAIFGDDKSFEKRNYPPGQHGMAKKRGKKSEYAVQLMEKQKAKYSYGILEKQFRNLFEKASATKGVTGEVLLQLCEARLDNVVFRMGIAPSRRGARQIVSHRHITVNGEVVNIPSYHLKPGDKVAVREKSKSLEAIERSLSNSSHVYEWITWNNDLKEGTFVSVPARLQIPENIKEQLIVELYNK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 5 polymer

description	30S ribosomal protein S5
formula_weight	18206.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	j

MSKYKNVELVKPSGLELKDRLVSVNRVTKVTKGGRAFGFSAIVVVGDENGVVGHGLGKSKDVSEAIAKAVEDAKKNLVRIPLNGQSVPHEQKGKFGGARVFLIPASHGTGVIAGGAVRSVLESVGIHDVLSKSQGSSNPHNVVKATFDALLQMRSAHTVAKQRGVSLEKVFKG

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 6 polymer

description	30S ribosomal protein S6
formula_weight	13376.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	k

MNHYETVFILNPVLSEVQVKETVTKFEEFLTSRGAEMVSKEDWGLKKMAYEIQNKKSGFYHLFEFKVAGEVLIAFETEFRRDERVMRFLTVSLDKHAISWAERRRAKLKSTKA

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 7 polymer

description	30S ribosomal protein S7
formula_weight	18493.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	l

MRKRAAKKRPLLPDPRFNDQLVTRFVNNLMWDGKKSTAFKVFYDAIDIIETKKQNDEKTSLEIWKDALTNVMPHVEVRSRRVGGATFQIPMQIRPDRKISMAMKWLILYARRRNEKSMAQRLASECLAAAKEEGAAVKKRMDTHKMAEANKAFSHFRF

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 8 polymer

description	30S ribosomal protein S8
formula_weight	14652.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	m

MYTDPIADYLTRVRNAVAANHKVVEIPASNLKKEITKILFDQGYILSYKFEQNTVQGSIKIALKYDKDTKEPVIKDIQRISKPGLRKYAGAAKLPRILNGLGIAIVSTSKGLMTGKQAKQLNVGGEVICYVY

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 9 polymer

description	30S ribosomal protein S9
formula_weight	14464.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	n

MGVIHKIGRRKTAVARVYVSEGTGNITVNKKEFATYFPTATLQYKVLQPLSMTENVNNFDVKVNVYGGGTTGQAEAVRMALARVMCEVNAENRGILKPEGLLTRDPRMVERKKFGQKKARKRFQFSKR

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 10 polymer

description	30S ribosomal protein S10
formula_weight	11446.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	o

MSQKIRIKLKSYDHMLVDKSAEKIVKTVKTTGAVVTGPIPLPTHKKLFTVLRSPHVNKKAREQFEVMSYKRLIDIYSSSSKTIDALMKLELPSGVEVEIKV

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 11 polymer

description	30S ribosomal protein S11
formula_weight	13701.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	p

MAKATAKKRKVIVESTGEAHISSTFNNIIISLTNKKGEVIAWSSAGKMGFRGSKKNTPYAAQMAAEDCSKVALEAGLKKVKVYVKGPGNGRESAIRSIHNGGIEVTEIIDVTPMPHNGCRPPKRRRV

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 12 polymer

description	Small ribosomal subunit protein uS12
formula_weight	14121.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	q

MPTIQQLVRTGRTQITKKSKSVALDSCPQRRGVCTRVYTTTPKKPNSAMRKVARVRLTNGNEVNAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYHIVRGALDTSGVAGRTQRRSKYGAKRPKEAKK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 13 polymer

description	30S ribosomal protein S13
formula_weight	13734.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	r

MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTVANKKKATK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 14 polymer

description	30S ribosomal protein S14
formula_weight	10211.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	s

MAKESMKAREVKREKTVAKYAEKRKALLEAGDYEGLQRLPKNASPVRLHNRCKLTGRPRGYIRQFGISRVTFREMANNGLIPGVKKASW

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 15 polymer

description	30S ribosomal protein S15
formula_weight	10565.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	t

MYLTKEKKEEIFAQHGDAKNTGKAEGQIALFTYRISHLTEHLKKNRHDYNTERSLVLLVGKRRALLDYLKRKDINRYREIIKVLNIRK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 16 polymer

description	Small ribosomal subunit protein bS16
formula_weight	20050.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	u

MSVKIRLQRHGKKGKPFYWVVAADARSKRDGKYLEKIGTYNPNTNPATVELNLDSAVKWLHNGAQPTDTARAILSYKGALLKHHLDGGVRKGALTQEQADAKLTAWLEAKAGKVDAKKDGLSKAQADAKAKALKAEKEVNDKRIAAAAKAEADAIAAASATEEAATEEVAEAAEEAPAAEENNETTEA

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 17 polymer

description	30S ribosomal protein S17
formula_weight	10108.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	v

MEEKRNLRKERIGVVTSNKMDKSIVISEVRKVKHPLYGKFVLKTKKYVAHDETNDCNIGDTVRISETRPLSKTKCWRLVEILERAK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 18 polymer

description	30S ribosomal protein S18
formula_weight	11378.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	w

MSTIEQSAKGKKDGDIRYLTPLNIETNKTKKYCRFKKSGIKYIDYKDADFLLKFVNEQGKILPRRLTGTSLKYQRKVSVAVKRARHLALMPYVADLLK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 19 polymer

description	30S ribosomal protein S19
formula_weight	10278.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	x

MARSLKKGPFVHYKLDKKVQENVESGKNSVVKTWSRASMITPDFVGQTIAVHNGRQFVPVYVTENMVGHKLGEFSPTRSFRGHAGAKNKGKK

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 20 polymer

description	30S ribosomal protein S20
formula_weight	9442.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	y

MANHKSALKRIRSNEKRRVLNRYQHKTTRNAIKALRLATDKSDAAAKLSTVISMIDKLAKKNIIHDNKASNLKSKLTKHVAKL

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 21 polymer

description	30S ribosomal protein S21
formula_weight	7433.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	z

MLIIPIKDGENIDRALKRYKRKFDKTGTVRQLRARTAFIKPSVVKRAQIQKAAYIQTLKDSLES

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

Entity 22 polymer

description	16S rRNA
formula_weight	491833.2 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	2

UAUACGAUGAAGAGUUUGAUCCUGGCUCAGGAUGAACGCUAGCGGCAGGCUUAACACAUGCAAGUCGAGGGGUAGAAGUCUUCGGGCUUUGAGACCGGCGCACGGGUGCGUAACGCGUAUGCAAUCUGCCUUUCACAGAGGGAUAGCCCAGAGAAAUUUGGAUUAAUACCUCAUAGUAUUAUAGAGCGGCAUCACUUUAUAAUUAAAGUCACAACGGUGAAAGAUGAGCAUGCGUCCCAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCCACGAUGGGUAGGGGUCCUGAGAGGGAGAUCCCCCACACUGGUACUGAGACACGGACCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAUGGACGCAAGUCUGAACCAGCCAUGCCGCGUGCAGGAUGACGGUCCUAUGGAUUGUAAACUGCUUUUGUACGAGAAGAAACACUCCUAUAUAUAGGAGCUUGACGGUAUCGUAAGAAUAAGGAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUCCAAGCGUUAUCCGGAAUCACUGGGUUUAAAGGGUCCGUAGGCGGUUUAGUAAGUCAGUGGUGAAAGCCCAUCGCUCAACGGUGGAACGGCCAUUGAUACUGCUGAACUUGAAUUACUGGGAAGUAACUAGAAUAUGUAGUGUAGCGGUGAAAUGCUUAGAUAUUACAUGGAAUACCAAUUGCGAAGGCAGGUUACUACCAGUUUAUUGACGCUGAUGGACGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGGAUACUAGCUGUUGGGCGCAAGUUCAGUGGCUAAGCGAAAGUGAUAAGUAUCCCACCUGGGGAGUACGAACGCAAGUUUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAACAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCAAGGCUUAAAUGCAGACUGACCGAUUUGGAAACAGAUCUUAUCGCAAGACAGUUUACAAGGUGCUGCAUGGUUGUCGUCAGCUCGUGCCGUGAGGUGUCAGGUUAAGUCCUAUAACGAGCGCAACCCCUGUUGUUAGUUGCCAGCGAGUGAUGUCGGGAACUCUAACAAGACUGCCAGUGCAAACUGUGAGGAAGGUGGGGAUGACGUCAAAUCAUCACGGCCCUUACGCCUUGGGCUACACACGUGCUACAAUGGCCGGUACAGAGAGCAGCCACUGGGUGACCAGGAGCGAAUCUAUAAAGCCGGUCACAGUUCGGAUCGGAGUCUGCAACUCGACUCCGUGAAGCUGGAAUCGCUAGUAAUCGGAUAUCAGCCAUGAUCCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGGAAGCUGGGGGUGCCUGAAGUCGGUGACCGCAAGGAGCUGCCUAGGGUAAAACUGGUAACUAGGGCUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAACACCUCCUUUCU

Source

organism	Flavobacterium johnsoniae
ncbi_taxonomy_id	986
host_organism	Flavobacterium johnsoniae

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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	2.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.70 Å
resolution_method	—
num_particles	431185

fit	/app/data/saxs_computation/zc/9zcd/9zcd.fit
pddf	/app/data/pr_computation/zc/9zcd/9zcd.pr.out
profile	/app/data/saxs_computation/zc/9zcd/9zcd.dat

Flavobacterium johnsoniae 30S 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

Refinement

EM 3D

5. Entities & Polymer Info (22)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

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Entity 3 polymer

Polymer

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Entity 4 polymer

Polymer

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Entity 5 polymer

Polymer

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Entity 6 polymer

Polymer

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Entity 7 polymer

Polymer

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Entity 8 polymer

Polymer

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Entity 9 polymer

Polymer

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Entity 10 polymer

Polymer

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Entity 11 polymer

Polymer

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Entity 12 polymer

Polymer

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Entity 13 polymer

Polymer

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Entity 14 polymer

Polymer

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Entity 15 polymer

Polymer

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Entity 16 polymer

Polymer

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Entity 17 polymer

Polymer

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Entity 18 polymer

Polymer

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Entity 19 polymer

Polymer

Source

Entity 20 polymer

Polymer

Source

Entity 21 polymer

Polymer

Source

Entity 22 polymer

Polymer

Source

6. Citations (1)