SAXSdb — 8g07

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8g07
沉积日期 deposition_date	2023-01-31
结构标题 title	Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase FO region
关键词 keywords	ATP synthase, mycobacterial, inhibitor, tuberculosis, antibiotic, HYDROLASE, TRANSLOCASE-INHIBITOR complex; TRANSLOCASE/INHIBITOR
实验方法 method	ELECTRON MICROSCOPY

▼

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

回转半径 Rg (Guinier) rg_guinier	28.88 Å
回转半径 Rg (电子) rg_electron	28.10 Å
零角强度 I(0) i0	139510000.00
分子量 molecular_weight	105460.0 kDa
排除体积 excluded_volume	136990 Å³
包络体积 envelope_volume	153920 Å³
水化壳体积 shell_volume	43614 Å³
包络直径 envelope_diameter	96.3 Å
壳层 Rg shell_rg	37.05 Å
包络 Rg envelope_rg	28.25 Å
形状 Rg shape_rg	28.09 Å
总 Rg total_rg	29.04 Å
总原子数 total_atoms	7467
残基数 n_residues	1045
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

▼

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

最大尺寸 Dmax dmax	92.3 Å
Rg (实空间) rg_real	28.74 Å
Rg 误差 (实空间) rg_real_error	0.68 Å
I(0) (实空间) i0_real	1.3950e+08
I(0) 误差 (实空间) i0_real_error	2.0640e+06
Rg (倒空间) rg_reciprocal	28.80 Å
I(0) (倒空间) i0_reciprocal	139500000.0000
解质量估计 total_estimate	0.8883
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	33.6 Å
偏度 Skewness skewness	0.195
峰度 Kurtosis kurtosis	-0.393
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13610000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.960

▶

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

▶

5. 实体与聚合体信息 (5)

Entity 1 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	1,2,3,4,5,6,7,8,9
原子数 atom_count	7467

MDLDPNAIITAGALIGGGLIMGGGAIGAGIGDGIAGNALISGIARQPEAQGRLFTPFFITVGLVEAAYFINLAFMALFVFATPGLQ

Entity 2 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 3 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 4 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 5 non-polymer

描述 description	3-[4-(morpholin-4-yl)phenyl]-4-{[(pyridin-2-yl)methyl]amino}cyclobut-3-ene-1,2-dione
分子量 formula_weight	349.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

▼

6. 折叠分类 (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

结构域编号 domain_id	8g07101
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

结构域编号 domain_id	8g07201
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

结构域编号 domain_id	8g07301
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

结构域编号 domain_id	8g07401
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

结构域编号 domain_id	8g07501
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

结构域编号 domain_id	8g07601
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

结构域编号 domain_id	8g07701
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

结构域编号 domain_id	8g07801
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

结构域编号 domain_id	8g07901
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	20 — F1FO ATP Synthase
同源超家族 H-superfamily homologous superfamily	10 — F1F0 ATP synthase subunit C

▶

7. 引用文献 (1)

▶

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	2.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	228696

fit	/app/data/saxs_computation/g0/8g07/8g07.fit
pddf	/app/data/pr_computation/g0/8g07/8g07.pr.out
profile	/app/data/saxs_computation/g0/8g07/8g07.dat

Cryo-EM structure of SQ31f-bound Mycobacterium smegmatis ATP synthase FO region

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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (5)

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 non-polymer

6. 折叠分类 (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)