8g0e

Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 3

Method: ELECTRON MICROSCOPY D_max: 204.9 Å Quality: REASONABLE

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	8g0e
沉积日期 deposition_date	2023-01-31
结构标题 title	Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 3
关键词 keywords	ATP synthase, mycobacterial, inhibitor, tuberculosis, antibiotic, HYDROLASE, TRANSLOCASE-INHIBITOR complex; TRANSLOCASE/INHIBITOR
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	62.02 Å
回转半径 Rg (电子) rg_electron	64.11 Å
零角强度 I(0) i0	3503580000.00
分子量 molecular_weight	510390.0 kDa
排除体积 excluded_volume	644030 Å³
包络体积 envelope_volume	870510 Å³
水化壳体积 shell_volume	119130 Å³
包络直径 envelope_diameter	233.5 Å
壳层 Rg shell_rg	60.69 Å
包络 Rg envelope_rg	63.41 Å
形状 Rg shape_rg	64.14 Å
总 Rg total_rg	63.93 Å
总原子数 total_atoms	35959
残基数 n_residues	4858
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	204.9 Å
Rg (实空间) rg_real	62.66 Å
Rg 误差 (实空间) rg_real_error	1.46 Å
I(0) (实空间) i0_real	3.5000e+09
I(0) 误差 (实空间) i0_real_error	7.4420e+07
Rg (倒空间) rg_reciprocal	61.32 Å
I(0) (倒空间) i0_reciprocal	3495000000.0000
解质量估计 total_estimate	0.5585
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	57.4 Å
偏度 Skewness skewness	0.633
峰度 Kurtosis kurtosis	-0.225
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0039
最高正则化参数 α highest_alpha	383900000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.679; Stabil: 0.999; Sysdev: 0.004; Positv: 1.000; Valcen: 0.991; Smooth: 0.217

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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 (12)

Entity 1 polymer

描述 description	ATP synthase subunit alpha
分子量 formula_weight	58951.5 kDa
EC 编号 ec_number	7.1.2.2
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	35959

MAELTISAADIEGAIEDYVSSFSADTEREEIGTVIDAGDGIAHVEGLPSVMTQELLEFPGGVLGVALNLDEHSVGAVILGEFEKIEEGQQVKRTGEVLSVPVGDAFLGRVVNPLGQPIDGQGDIAAETRRALELQAPSVVQRQSVSEPLQTGIKAIDAMTPIGRGQRQLIIGDRKTGKTAVCVDTILNQREAWLTGDPKQQVRCVYVAIGQKGTTIASVKRALEEGGAMEYTTIVAAPASDAAGFKWLAPYTGSAIGQHWMYNGKHVLIVFDDLSKQADAYRAISLLLRRPPGREAFPGDVFYLHSRLLERCAKLSDELGGGSMTGLPIIETKANDISAFIPTNVISITDGQCFLESDLFNQGVRPAINVGVSVSRVGGAAQIKAMKEVAGSLRLDLSQYRELEAFAAFASDLDAASKAQLDRGARLVELLKQPQYSPLAVEEQVVAIFLGTQGHLDSVPVEDVQRFESELLEHVKASHSDIFDGIRETKKLSEEAEEKLVSVINEFKKGFQASDGSSVVVSENAEALDPEDLEKESVKVRKPAPKKA

Entity 2 polymer

描述 description	ATP synthase subunit beta
分子量 formula_weight	51670.5 kDa
EC 编号 ec_number	7.1.2.2
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

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

MTATAEKTAGRVVRITGPVVDVEFPRGSVPELFNALHAEITFGALAKTLTLEVAQHLGDSLVRCISMQPTDGLVRGVEVTDTGASISVPVGDGVKGHVFNALGDCLDDPGYGKDFEHWSIHRKPPAFSDLEPRTEMLETGLKVVDLLTPYVRGGKIALFGGAGVGKTVLIQEMINRIARNFGGTSVFAGVGERTREGNDLWVELADANVLKDTALVFGQMDEPPGTRMRVALSALTMAEFFRDEQGQDVLLFIDNIFRFTQAGSEVSTLLGRMPSAVGYQPTLADEMGELQERITSTRGRSITSMQAVYVPADDYTDPAPATTFAHLDATTELSRAVFSKGIFPAVDPLASSSTILDPAIVGDEHYRVAQEVIRILQRYKDLQDIIAILGIDELSEEDKQLVNRARRIERFLSQNMMAAEQFTGQPGSTVPLKETIEAFDKLTKGEFDHLPEQAFFLIGGLDDLAKKAESLGAKL

Entity 3 polymer

描述 description	ATP synthase gamma chain
分子量 formula_weight	33439.8 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

MAATLRELRGRIRSAGSIKKITKAQELIATSRIAKAQARVEAARPYAAEITNMLTELAGASALDHPLLVERKQPKRAGVLVVSSDRGLCGAYNANVLRRAEELFSLLRDEGKDPVLYVVGRKALGYFSFRQRTVVESWTGFSERPTYENAREIADTLVNAFMAGADDEGDDAGADGILGVDELHIVFTEFRSMLSQTAVARRAAPMEVEYVGEVETGPRTLYSFEPDPETLFDALLPRYIATRVYAALLEAAASESASRRRAMKSATDNADDLIKALTLAANRERQAQITQEISEIVGGANALAGSK

Entity 4 polymer

描述 description	ATP synthase epsilon chain
分子量 formula_weight	13277.7 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	H

MADLNVEIVAVERELWSGPATFVFTRTTAGEIGILPRHIPLVAQLVDDAMVRVEREGEDDLRIAVDGGFLSVTEETVRILVENAQFESEIDADAAKEDAASDDERTAAWGRARLRALGQID

Entity 5 polymer

描述 description	ATP synthase subunit b
分子量 formula_weight	17636.7 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	b

MGEFSATILAASQAAEEGGGGSNFLIPNGTFFAVLIIFLIVLGVISKWVVPPISKVLAEREAMLAKTAADNRKSAEQVAAAQADYEKEMAEARAQASALRDEARAAGRSVVDEKRAQASGEVAQTLTQADQQLSAQGDQVRSGLESSVDGLSAKLASRILGVDVNSGGTQ

Entity 6 polymer

描述 description	ATP synthase subunit b-delta
分子量 formula_weight	47504.7 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	d

MSIFIGQLIGFAVIAFIIVKWVVPPVRTLMRNQQEAVRAALAESAEAAKKLADADAMHAKALADAKAESEKVTEEAKQDSERIAAQLSEQAGSEAERIKAQGAQQIQLMRQQLIRQLRTGLGAEAVNKAAEIVRAHVADPQAQSATVDRFLSELEQMAPSSVVIDTAATSRLRAASRQSLAALVEKFDSVAGGLDADGLTNLADELASVAKLLLSETALNKHLAEPTDDSAPKVRLLERLLSDKVSATTLDLLRTAVSNRWSTESNLIDAVEHTARLALLKRAEIAGEVDEVEEQLFRFGRVLDAEPRLSALLSDYTTPAEGRVALLDKALTGRPGVNQTAAALLSQTVGLLRGERADEAVIDLAELAVSRRGEVVAHVSAAAELSDAQRTRLTEVLSRIYGRPVSVQLHVDPELLGGLSITVGDEVIDGSIASRLAAAQTGLPD

Entity 7 polymer

描述 description	ATP synthase subunit c
分子量 formula_weight	8598.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	9

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	9,1,2,3,4,5,6,7,8

MDLDPNAIITAGALIGGGLIMGGGAIGAGIGDGIAGNALISGIARQPEAQGRLFTPFFITVGLVEAAYFINLAFMALFVFATPGLQ

Entity 8 polymer

描述 description	ATP synthase subunit a
分子量 formula_weight	27568.5 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	a

MLAAEEGGAAIHVGHHTLVFELFGMTFNGDTILATAVTAVIVIALAFYLRAKVTSTGVPSGVQLFWEALTIQMRQQIEGSIGMKIAPFVLPLSVTIFVFILISNWLAVLPLQYGGADGAAAELYKAPASDINFVLALALFVFVCYHAAGIWRRGIVGHPIKVVKGHVAFLAPINIVEELAKPISLALRLFGNIFAGGILVALIAMFPWYIQWFPNAVWKTFDLFVGLIQAFIFSLLTILYFSQSMELDHEDH

Entity 9 non-polymer

描述 description	ADENOSINE-5'-TRIPHOSPHATE
分子量 formula_weight	507.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 10 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 11 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 non-polymer

描述 description	;(1R,2S)-1-(6-bromo-2-methoxyquinolin-3-yl)-2-(2,6-dimethoxypyridin-4-yl)-4-(dimethylamino)-1-(2,3,6-trimethoxypyridin-4-yl)butan-2-ol ;
分子量 formula_weight	657.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

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7. 引用文献 (1)

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分辨率 resolution	2.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	166169

fit	/app/data/saxs_computation/g0/8g0e/8g0e.fit
pddf	/app/data/pr_computation/g0/8g0e/8g0e.pr.out
profile	/app/data/saxs_computation/g0/8g0e/8g0e.dat

Cryo-EM structure of TBAJ-876-bound Mycobacterium smegmatis ATP synthase rotational state 3

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (12)

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 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)