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9t61

Doxycycline Bound C. burnetii 30S Ribosome

Method: ELECTRON MICROSCOPY D_max: 211.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t61
deposition_date	2025-11-06
title	Doxycycline Bound C. burnetii 30S Ribosome
keywords	Ribosome, C. burnetii, 30S subunit, antibiotic, doxycycline, pathogen, cryo-EM; 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	67.01 Å
rg_electron	67.45 Å
i0	18365400000.00
molecular_weight	761120.0 kDa
excluded_volume	791990 Å³
envelope_volume	1306800 Å³
shell_volume	160110 Å³
envelope_diameter	238.7 Å
shell_rg	67.79 Å
envelope_rg	66.74 Å
shape_rg	67.46 Å
total_rg	67.43 Å
total_atoms	51196
n_residues	3783
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	211.8 Å
rg_real	67.06 Å
rg_real_error	1.40 Å
i0_real	1.8360e+10
i0_real_error	4.0160e+08
rg_reciprocal	66.55 Å
i0_reciprocal	18350000000.0000
total_estimate	0.8398
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	73.7 Å
skewness	0.427
kurtosis	-0.342
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0015
highest_alpha	1526000000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.124

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4. Crystallography & Experiment

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5. Entities & Polymer Info (27)

Entity 1 polymer

description	Large ribosomal subunit protein bL31
formula_weight	9096.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	4
atom_count	51204

MKENIHPPYKQIKVTCSCGNTFMTGSTLDRELHLEICSACHPFYTGQQKMVDTAGRVERFRKKYAKRRAANASPEDEKK

Entity 2 polymer

description	16S ribosomal RNA
formula_weight	497437.7 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A

AAUUGAAGAGUUUGAUUCUGGCUCAGAUUGAACGCUAGCGGCAUGCUUAACACAUGCAAGUCGAACGGCAGCGCGGGGAGCUUGCUCCCUGGCGGCGAGUGGCGGACGGGUGAGUAAUGCGUAGGAAUCUACCUUGUAGUGGGGGAUAACCUGGGGAAACUCGGGCUAAUACCGCAUAAUCUCUUUGGAGCAAAGCGGGGGAUCUUCGGACCUCGUGCUAUAAGAUGAGCCUACGUCGGAUUAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGAUCCGUAGCUGGUCUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGAAACCCUGAUCCAGCAAUGCCGCGUGUGUGAAGAAGGCCUUCGGGUUGUAAAGCACUUUCGGUGGGGAAGAAAUUCUCAAGGGUAAUAUCCUUGGGCGUUGACGUUACCCACAGAAGAAGCACUGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGAGUGCAAGCGUUAAUCGGAAUCACUGGGCGUAAAGCGCGCGUAGGUGGAUAUUUAAGUCGGAUGUGAAAGCCCUGGGCUUAACCUGGGAAUUGCACCCGAUACUGGGUAUCUUGAGUAUGGUAGAGGGAAGUGGAAUUUCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGAAAGAACACCAGUGGCGAAGGCGACUUCCUGGACCAAUACUGACACUGAGGCGCGAAAGCGUGGGGAGCAAACAGGAUUAGAGACCCUGGUAGUCCACGCCGUCAACGAUGAGAACUAGCUGUUGGGAAGUUCACUUCUUAGUAGCGAAGCUAACGCGUUAAGUUCUCCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAGAAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAAAACCUUACCUACCCUUGACAUCCUCGGAACUUGUCAGAGAUGAUUUGGUGCCUUCGGGAACCGAGUGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGUAACGAGCGCAACCCUCGUCCUUAGUUGCCAGCGAGUCAAGUCGGGAACUCUAAGGAGACUGCCGGUGAUAAACCGGAGGAAGGUGGGGAUGAUGUCAAGUCAUCAUGGCCCUUACGGGUAGGGCUACACACGUGCUACAAUGGGCAGUACAAAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCCCAGAAAACUGCUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUUGGAAUCGCUAGUAAUCGCGAAUCAGCAUGUCGCGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGAAUUGUACCAGAAGCGGGUAGGCUAACCUUCGGGAGGCCGCUCACCACGGUAUGAUCCAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUC

Entity 3 polymer

description	Small ribosomal subunit protein uS3
formula_weight	25671.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MGQKVNPVGMRIGITRDWTSNWYADKKDFADRLNEDLNVRQLLQKRLKGAAVSRIQIERPARNAKIIIHSARPGVIIGKKGGEIEALRDEIFKVMKVPVHITIEEVRKPELDAKLVAENIAQQLERRVMFRRAMKRAVQNTLRQGALGVKISVSGRLGGAEIARTEWYREGRVPLHTFRADIDYATASAKTTYGIIGVKVWIFKGEVHAPKPQAEEAAPQETEEEVK

Entity 4 polymer

description	Small ribosomal subunit protein uS4
formula_weight	23770.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MARYLGPKCRLSRREKTDLQLKSGIRAIDSKCNIERIPGMHWQRRGRTTDYGVQLRMKQMIKRYYDVLEKQFANYYKQADRLKGSTGDNLLKLLESRLDNVVYRMGFAATRAEARQLISHKAILVNGEVVNIPSYQVKPGDIIEVRSRAKGQLRIKGALELAQQRAPISWIEVDTKKMTGTFKEQPDVAELPAEFKVNLVVELYSK

Entity 5 polymer

description	Small ribosomal subunit protein uS5
formula_weight	17510.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MQEAGIGTTTDGIQEKLVAVRRTAKVVKGGRVFGFSALVVAGDGDGKVGFGLGKAREVPSAIQKATENARRNMISVPLYGATLHHAIKATHASSTVLMLPASEGTGVIAGNAMRAIFEVMGVQNVLAKCIGSSNPINVVRATFKGLKQMETPESVAAKRGKAIEEIVE

Entity 6 polymer

description	Small ribosomal subunit protein bS6
formula_weight	14603.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MRHYEIVILVHPDQSSQVPAMVERYQSMIKEKDGKVHRLEDWGRRQLAYSIDKVHKAHYLLMNIESDQGVISELENAFRYNDAVIRSLILKRDHAITKSSLIMQGAEKGKSSRKEKVAAEAEASEEA

Entity 7 polymer

description	Small ribosomal subunit protein uS7
formula_weight	21334.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MARRKAAPKRETLPDPLFHSELLAKFINAVMRNGKKSVAEKIVYGALDVVAKRVQNKSGEQGDGDGESGGKAGGIKKRSLGDIRTDENARALALETFKGALDKVMPNVEVKSRRVGGSTYQVPVEIRMARRQALARRWLVEYANKRNEKTMVLRLAHEILDAVEGRGGAIKKREDVHRMAKANQAFAHYKW

Entity 8 polymer

description	Small ribosomal subunit protein uS8
formula_weight	14592.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MMQDPISDMLTRIRNAQAVRKKEVVMPRSKLKMSIANVLKEEGYIVDYREEGDLTKAQLVITLKYHEGESVISEIRRVSSPALQVYKSKDELPKVKNGLGIAIISTSKGVMSDRQARRLGEGGEVLCYVS

Entity 9 polymer

description	Small ribosomal subunit protein uS9
formula_weight	15332.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MAQAAKKQNLGTGRRKTSSARVFLRSGTGQIIINGLPLDEYFGRETARMVVRQPLVKLDVQSRFDVYATVQGGGDSGQAGAIRHGITRALIQYDEEGGEGGTWRSTLRKAGFVTRDPRMVERKKVGLHGARRGTQFSKR

Entity 10 polymer

description	Small ribosomal subunit protein uS11
formula_weight	13534.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MAKKRYRKVTEGIAHIKATFNNTMISVSDPQGNVLCFRSAGGSGFKGSRKGTPYGAQMASEEVGRLARDNFDMRRIAVRVKGPGAGRDSAIRGLRSAGLEVIHLEDRTPLPHNGCRPRKKRRV

Entity 11 polymer

description	Small ribosomal subunit protein uS12
formula_weight	13786.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MARINQLVRKPRRARAKKSDVPALEGCPQRRGVCTRVYTTTPKKPNSALRKVARVRITNGAEVTAYIGGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGSLDTAGVSGRRRGRSKYGEKKPKE

Entity 12 polymer

description	Small ribosomal subunit protein uS13
formula_weight	13420.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MAARIAGVNIPVQKHARIALQAIYGIGNSRALEICKEAKIDPATKVKDLSEAELDALRTEVGKFSVEGDLRRERSMDIKRKMDLGAYEGIRHRRGLPLRGQRTRSNARTRKGKRKPIRS

Entity 13 polymer

description	Small ribosomal subunit protein uS14
formula_weight	11600.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MAKLSVIERNKKRVRKSQSARKKRLELKKIIKKGTPEEQEQALLKLQKRPRDESPVRTRDRCRLCGRPCGTFKKFGLCRIHLREAAMRADVPGLKKASW

Entity 14 polymer

description	Small ribosomal subunit protein uS15
formula_weight	10340.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	O

MSLASAETAKIVKEYQLGKDDTGSPEVQVAILTAKIIKLTDHMKAHKHDHHSRRGLLRMVSQRRKLLNFLKRNDLQRYLKLIERLGLRS

Entity 15 polymer

description	Small ribosomal subunit protein bS16
formula_weight	15592.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

MVVIRLARGGSKKNPFYHIVVADRRKPRDGRFIERVGYYNPMARGQDIRLQLEKERISHWLNQGAQTSLRVKHLIKKLEKSPEEAQKGGMRKGEFKRLQAEQAAKAQKKAVATEEPKAEEAKEAPPAESQAAEGKEE

Entity 16 polymer

description	Small ribosomal subunit protein uS17
formula_weight	10328.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Q

MNKNEKMVRSLMGTVVSNKMNDTVVVRVERRVKHPKYGKFIKRSTKIHAHDKGNEGQIGDIVTIRECRPISKTKSWTLVKINERAEKVE

Entity 17 polymer

description	Small ribosomal subunit protein bS18
formula_weight	8569.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

MSFRRKKFCAFDAKNLQEIDYKDVNTLKDYIMESGRVVPSRITGTCAKHQRQISRAIKLARYLALLPYCDTHQ

Entity 18 polymer

description	Small ribosomal subunit protein uS19
formula_weight	10842.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

MPRSTNKGPFVDHHLMKKVDQAQKEGSKRPIKTWSRRSMVVPEMVGLTIAIHNGRQHVPVYISENMVGHKLGEFAITRTFRAHSGDRKAKKEGEK

Entity 19 polymer

description	Small ribosomal subunit protein bS20
formula_weight	9981.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	T

MANSAQAKKRARQNEKRELHNASQRSAVRTAVKKILKSLQANDSSAAQSAYQHAVQILDKAAGRRIIHPNKAARLKSRLSQKIKNLSSSQ

Entity 20 polymer

description	Small ribosomal subunit protein bS21
formula_weight	8927.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	U

MPMIDVPDNNAFDVAMRRFKRACEKAGILSKLRQIEYYEKPTSKRKRKRAAAVKRYAKKLQKEQEALERERTRY

Entity 21 polymer

description	P-site tRNA-Met
formula_weight	24749.7 kDa
src_method	nat
entity_count	1

Polymer

type	polyribonucleotide
strand_id	Y

UGCGGGGUGGAGCAGUCUGGCAGCUCGUCGGGCUCAUAACCCGAAGGUCGUAGGUUCAAAUCCUACCCCCGCUACCA

Entity 22 polymer

description	Small ribosomal subunit protein uS10
formula_weight	12614.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MSDNQRIRIRLKAFDHRLIDRSTREIVETARRTGAIIRGPILLPTKIERYTVLISPNIDKDARDQYEIRTHKRLVDISEPTDKTVDALMKLDLAAGVDVQIELLNKKSGA

Entity 23 non-polymer

description	;(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE ;
formula_weight	444.4 kDa
src_method	syn
entity_count	1

Entity 24 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	34

Entity 25 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	54

Entity 26 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 27 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	8

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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	3.06 Å
resolution_method	—
num_particles	10803

fit	/app/data/saxs_computation/t6/9t61/9t61.fit
pddf	/app/data/pr_computation/t6/9t61/9t61.pr.out
profile	/app/data/saxs_computation/t6/9t61/9t61.dat

Doxycycline Bound C. burnetii 30S Ribosome

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 (27)

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

Entity 23 non-polymer

Entity 24 non-polymer

Entity 25 non-polymer

Entity 26 non-polymer

Entity 27 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)