9h90

Cryo-EM structure of the Vibrio natrigens 30S ribosomal subunit in complex with spectinomycin.

Method: ELECTRON MICROSCOPY D_max: 220.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9h90
沉积日期 deposition_date	2024-10-29
最后修订 last_revision	2025-05-21
结构标题 title	Cryo-EM structure of the Vibrio natrigens 30S ribosomal subunit in complex with spectinomycin.
关键词 keywords	Vibrio natriegens, Ribosome, Bac5, Bactenecin 5, 50S, V. natriegens; RIBOSOME
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	65.05 Å
回转半径 Rg (电子) rg_electron	65.37 Å
零角强度 I(0) i0	16419300000.00
分子量 molecular_weight	705410.0 kDa
排除体积 excluded_volume	725670 Å³
包络体积 envelope_volume	1174000 Å³
水化壳体积 shell_volume	149200 Å³
包络直径 envelope_diameter	237.7 Å
壳层 Rg shell_rg	65.48 Å
包络 Rg envelope_rg	64.61 Å
形状 Rg shape_rg	65.34 Å
总 Rg total_rg	65.41 Å
总原子数 total_atoms	47459
残基数 n_residues	3433
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	220.5 Å
Rg (实空间) rg_real	65.31 Å
Rg 误差 (实空间) rg_real_error	2.26 Å
I(0) (实空间) i0_real	1.6420e+10
I(0) 误差 (实空间) i0_real_error	3.3400e+08
Rg (倒空间) rg_reciprocal	64.79 Å
I(0) (倒空间) i0_reciprocal	16400000000.0000
解质量估计 total_estimate	0.8446
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	64.3 Å
偏度 Skewness skewness	0.439
峰度 Kurtosis kurtosis	-0.287
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1119000000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.432

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (20)

Entity 1 polymer

描述 description	30S ribosomal protein S21
分子量 formula_weight	8512.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	u
原子数 atom_count	47463

MPVVKVRENEPFDVALRRFKRSCEKAGILSEVRRREHYEKPTTVRKRAKAAAQKRHAKKLARENARRVRLY

Entity 2 polymer

描述 description	30S ribosomal protein S3
分子量 formula_weight	25598.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

MGQKVHPNGIRLGIVKPWNATWFANTKDFADNLDGDFKVRQFLTGELKKASLSRIVIERPAKSIRVTIHTARPGVVIGKKGEDVEKLRAAVAKIAGVPAQINIAEVRKPELDAQLVGDSIASQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARSEWYREGRVPLHTLRADIDYATSSAHTQYGVIGIKTWIFKGEILGGMPAANAVEPKGDKPKKQRKGRK

Entity 3 polymer

描述 description	Small ribosomal subunit protein uS7
分子量 formula_weight	17765.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G

MPRRRVIGQRKILPDPKFKSELLAKFVNILMVDGKKSTAEKIVYTALDAMAEKSGKDHLAIFEEALENVRPAVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWLVEAARKRGEKSMAQRLAAEMLDASENKGTAVKKREDVHRMADANKAFAHYRW

Entity 4 polymer

描述 description	30S ribosomal protein S15
分子量 formula_weight	10084.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	o

MSLNAETKAAIVAEYAQSEGDTGSPEVQVALLTASINHLQGHFKAHKGDHHSRRGLLRMVSRRRKLLDYLKGKNLARYQDLIKRLGLRR

Entity 5 polymer

描述 description	30S ribosomal protein S8
分子量 formula_weight	14027.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	h

MSMQDPISDMLTRVRNGQAANKVAVKMPSSKLKVAIAALLKAEGYIVDFAVEGEAKPELEVTLKYFQAKPVIEQLKRVSRPGLRVYKKKDQLPSVMGGLGIAIVSTSKGLMSDRAARKAGLGGEIICYVA

Entity 6 polymer

描述 description	30S ribosomal protein S6
分子量 formula_weight	14994.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	f

MRHYEIVFMVHPDQSEQVAGMIERYTGSITEAGGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEADQAVIDELETAFRFNDAVLRNMVMRTKAAITEQSIMLKQKEERAPRREERSEAKPEAKSEAAE

Entity 7 polymer

描述 description	30S ribosomal protein S5
分子量 formula_weight	17609.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	e

MAKEQQVQANDLQEKLIAVNRVSKTVKGGRIMSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMTTIALNEGTLHHPVKGRHSGSKVYMQPAAEGTGVIAGGAMRAVLEVAGVHNVLSKAYGSTNPINIVRATIDALGSMKSPEMVAAKRGLTVESISE

Entity 8 polymer

描述 description	30S ribosomal protein S4
分子量 formula_weight	23392.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	d

MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIDNAPGVHGARRGRLSEYGVQLREKQKVRRMYGVLEKQFRNYYKEAARLKGNTGENLLQLLEGRLDNVVYRMGFGATRAEARQLVSHKAILVNGKVVNVPSFKVAANDVVSIREKAKQQSRIKAALEVAEQREKPTWIEVDGGKMEGTFKRMPERSDLSADINEQLIVELYSK

Entity 9 polymer

描述 description	30S ribosomal protein S9
分子量 formula_weight	14638.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I

MAENQYYGTGRRKSSAARVFIKPGSGNIVVNKRNLDEYFGRPTARMVVQQPLELVELTDKLDLYVTVKGGGISGQAGAIRHGITRALMEYDESLRPALRAAGYVTRDARCVERKKVGLRKARRRPQFSKR

Entity 10 polymer

描述 description	16S ribosomal RNA
分子量 formula_weight	500566.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	a

AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAGCGGAAACGAGUUAUCUGAACCUUCGGGGAACGAUAACGGCGUCGAGCGGCGGACGGGUGAGUAAUGCCUAGGAAAUUGCCCUGAUGUGGGGGAUAACCAUUGGAAACGAUGGCUAAUACCGCAUGAUGCCUACGGGCCAAAGAGGGGGACCUUCGGGCCUCUCGCGUCAGGAUAUGCCUAGGUGGGAUUAGCUAGUUGGUGAGGUAAGGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUGUGAAGAAGGCCUUCGGGUUGUAAAGCACUUUCAGUCGUGAGGAAGGUAGUGUAGUUAAUAGCUGCAUUAUUUGACGUUAGCGACAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCGAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCAUGCAGGUGGUUUGUUAAGUCAGAUGUGAAAGCCCGGGGCUCAACCUCGGAAUAGCAUUUGAAACUGGCAGACUAGAGUACUGUAGAGGGGGGUAGAAUUUCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGAAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACAGAUACUGACACUCAGAUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCUACUUGGAGGUUGUGGCCUUGAGCCGUGGCUUUCGGAGCUAACGCGUUAAGUAGACCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCAGAGAACUUUUCAGAGAUGAAUUGGUGCCUUCGGGAACUCUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUGUUUGCCAGCGAGUAAUGUCGGGAACUCCAGGGAGACUGCCGGUGAUAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCGCAUACAGAGGGCGGCCAACUUGCGAAAGUGAGCGAAUCCCAAAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGCUGCAAAAGAAGUAGGUAGUUUAACCUUCGGGGGGACGCUUACCACUUUGUGGUUCAUGACUGGGGUGAAGUCGUAACAAGGUAGCGCUAGGGGAACCUGGCGCUGGAUC

Entity 11 polymer

描述 description	30S ribosomal protein S20
分子量 formula_weight	9590.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	t

MANSKSAKKRAIQAEKRRQHNASRRSMMRTYMKKTVAAIEAGDKEAATAAFAVVTPILDRMATKGLIHKNKAARHKSRFTAQIKAL

Entity 12 polymer

描述 description	30S ribosomal protein S18
分子量 formula_weight	8861.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	r

MARFFRRRKFCRFTAEGVQEIDYKDVATLKNYITEAGKIVPSRITGTSAKYQRQLARAIKRSRYLALLPYTDKHQ

Entity 13 polymer

描述 description	30S ribosomal protein S17
分子量 formula_weight	9605.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	q

MSEVKRTQQGRVVSDKMDKSITVAIERFVKHPIYGKYVKRTTKVHAHDENNECGLGDTVEIAECRPLSKTKSWTLVKVLEKAKI

Entity 14 polymer

描述 description	30S ribosomal protein S16
分子量 formula_weight	9080.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	p

MVTIRLARHGAKKRPFYQIVVADSRNAATGRFIEKVGFFNPTAKGQEEGLRLDLDRVNHWVGQGASVSDRVAKLVKDAQKAA

Entity 15 polymer

描述 description	30S ribosomal protein S12
分子量 formula_weight	13738.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	l

MATINQLVRKPRAKQVVKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVVLIRGGRVKDLPGVRYHTVRGALDCAGVNDRKQGRSKYGVKRPKS

Entity 16 polymer

描述 description	30S ribosomal protein S11
分子量 formula_weight	13916.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	k

MAKQPTRARKRVRKQVADGVAHIHASFNNTIVTITDRQGNALAWATAGGSGFRGSRKSTPFAAQVAAERCAEMAKEYGLKNLEVMVKGPGPGRESTVRALNAAGFRITNIVDATPIPHNGCRPPKKRRV

Entity 17 polymer

描述 description	30S ribosomal protein S14
分子量 formula_weight	11481.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

MAKNSMKAREAKRAKLVAKFAEKRSALKAIISDVNASEEDRWNAVLKLQSLPRDSSASRQRNRCNQTGRPHGYLRKFGLSRIKVREACMKGEIPGLRKASW

Entity 18 polymer

描述 description	30S ribosomal protein S10
分子量 formula_weight	11741.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J

MQNQRIRIRLKAFDYKLIDASTAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKKARDQYEIRTHKRLIDIVEPTDKTVDALMRLDLAAGVDVQISLG

Entity 19 non-polymer

描述 description	SPECTINOMYCIN
分子量 formula_weight	332.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 20 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	233.420 Å
R 因子 r_factor	0.3181
R_work r_work	0.3181
R_free r_free	—

分辨率 resolution	2.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	294068

fit	/app/data/saxs_computation/h9/9h90/9h90.fit
pddf	/app/data/pr_computation/h9/9h90/9h90.pr.out
profile	/app/data/saxs_computation/h9/9h90/9h90.dat

Cryo-EM structure of the Vibrio natrigens 30S ribosomal subunit in complex with spectinomycin.

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (20)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

Entity 12 polymer

聚合体 Polymer

Entity 13 polymer

聚合体 Polymer

Entity 14 polymer

聚合体 Polymer

Entity 15 polymer

聚合体 Polymer

Entity 16 polymer

聚合体 Polymer

Entity 17 polymer

聚合体 Polymer

Entity 18 polymer

聚合体 Polymer

Entity 19 non-polymer

Entity 20 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)