8hhb

F1 domain of FoF1-ATPase from Bacillus PS3,step waiting,lowATP

Method: ELECTRON MICROSCOPY D_max: 137.4 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	8hhb
沉积日期 deposition_date	2022-11-16
结构标题 title	F1 domain of FoF1-ATPase from Bacillus PS3,step waiting,lowATP
关键词 keywords	ATP synthase F1 ATPase FoF1, MOTOR PROTEIN; MOTOR PROTEIN
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	44.31 Å
回转半径 Rg (电子) rg_electron	43.50 Å
零角强度 I(0) i0	1715130000.00
分子量 molecular_weight	344760.0 kDa
排除体积 excluded_volume	432340 Å³
包络体积 envelope_volume	576550 Å³
水化壳体积 shell_volume	103000 Å³
包络直径 envelope_diameter	151.6 Å
壳层 Rg shell_rg	53.84 Å
包络 Rg envelope_rg	43.03 Å
形状 Rg shape_rg	43.52 Å
总 Rg total_rg	43.85 Å
总原子数 total_atoms	24245
残基数 n_residues	3129
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	137.4 Å
Rg (实空间) rg_real	43.99 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	1.7150e+09
I(0) 误差 (实空间) i0_real_error	2.7180e+07
Rg (倒空间) rg_reciprocal	44.30 Å
I(0) (倒空间) i0_reciprocal	1716000000.0000
解质量估计 total_estimate	0.6537
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	57.2 Å
偏度 Skewness skewness	0.100
峰度 Kurtosis kurtosis	-0.392
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	435300000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 0.005; Positv: 1.000; Valcen: 0.953; Smooth: 0.906

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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 (7)

Entity 1 polymer

描述 description	ATP synthase subunit alpha
分子量 formula_weight	54717.4 kDa
EC 编号 ec_number	7.1.2.2
来源方法 src_method	man
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	24245

SIRAEEISALIKQQIENYESQIQVSDVGTVIQVGDGIARAHGLDNVMSGELVEFANGVMGMALNLEENNVGIVILGPYTGIKEGDEVRRTGRIMEVPVGEALIGRVVNPLGQPVDGLGPVETTETRPIESPAPGVMDRRSVHEPLQTGIKAIDALVPIGRGQRELIIGDRQTGKTSVAIDTIINQKDQNMISIYVAIGQKESTVRTVVETLRKHGALDYTIVVTASASQPAPLLFLAPYAGVAMGEYFMYKGKHVLVVYDDLSKQAAAYRELSLLLRRPPGREAYPGDIFYLHSRLLERAAKLSDAKGGGSLTALPFVETQAGDISAYIPTNVISITDGQIFLQSDLFFSGVRPAINAGLSVSRVGGAAQIKAMKKVAGTLRLDLAAYRELEAFAQFGSDLDKATQAKLARGARTVEVLKQDLHQPIPVEKQVLIIYALTRGFLDDIPVEDVRRFEKEFYLFLDQNGQHLLEHIRTTKDLPNEDDLNKAIEAFKKTFVVSQ

来源 Source

来源生物 organism	Bacillus sp. PS3
NCBI 分类编号 ncbi_taxonomy_id	2334
宿主生物 host_organism	Escherichia coli K-12

Entity 2 polymer

描述 description	ATP synthase subunit beta
分子量 formula_weight	53424.6 kDa
EC 编号 ec_number	7.1.2.2
来源方法 src_method	man
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

MHHHHHHHHHHMTRGRVIQVMGPVVDVKFENGHLPAIYNALKIQHKARNENEVDIDLTLEVALHLGDDTVRTIAMASTDGLIRGMEVIDTGAPISVPVGEVTLGRVFNVLGEPIDLEGDIPADARRDPIHRPAPKFEELATEVEILETGIKVVDLLAPYIKGGKIGLFGGAGVGKTVLIQELIHNIAQEHGGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVALTGLTMAEYFRDEQGQDVLLFIDNIFRFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERITSTAKGSITSIQAIYVPADDYTDPAPATTFSHLDATTNLERKLAEMGIYPAVDPLASTSRALAPEIVGEEHYQVARKVQQTLQRYKELQDIIAILGMDELSDEDKLVVHRARRIQFFLSQNFHVAEQFTGQPGSYVPVKETVRGFKEILEGKYDHLPEDAFRLVGRIEEVVEKAKAMGVEV

来源 Source

来源生物 organism	Bacillus sp. PS3
NCBI 分类编号 ncbi_taxonomy_id	2334
宿主生物 host_organism	Escherichia coli K-12

Entity 3 polymer

描述 description	ATP synthase gamma chain
分子量 formula_weight	31728.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

ASLRDIKTRINATKKTSQITKAMEMVSTSKLNRAEQNAKSFVPYMEKIQEVVANVALGAGGASHPMLVSRPVKKTGYLVITSDRGLAGAYNSNVLRLVYQTIQKRHASPDEYAIIVIGRVGLSFFRKRNMPVILDITRLPDQPSFADIKEIARKTVGLFADGTFDELYMYYNHYVSAIQQEVTERKLLPLTDLAENKQRTVYEFEPSQEEILDVLLPQYAESLIYGALLDAKASEHAARMTAMKNATDNANELIRTLTLSYNRARQAAITQEITEIVAGANALQ

来源 Source

来源生物 organism	Bacillus sp. PS3
NCBI 分类编号 ncbi_taxonomy_id	2334
宿主生物 host_organism	Escherichia coli K-12

Entity 4 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 5 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	5

Entity 6 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 7 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

结构域编号 domain_id	8hhbA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8hhbB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8hhbC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8hhbD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	8hhbD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8hhbD03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
同源超家族 H-superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

结构域编号 domain_id	8hhbE01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	8hhbE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8hhbE03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
同源超家族 H-superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

结构域编号 domain_id	8hhbF01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	8hhbF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	8hhbF03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
同源超家族 H-superfamily homologous superfamily	10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3

结构域编号 domain_id	8hhbG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1380 — Pyruvate Kinase; Chain: A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — ATP synthase, F1 complex, gamma subunit

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7. 引用文献 (1)

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分辨率 resolution	3.50 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	7818

fit	/app/data/saxs_computation/hh/8hhb/8hhb.fit
pddf	/app/data/pr_computation/hh/8hhb/8hhb.pr.out
profile	/app/data/saxs_computation/hh/8hhb/8hhb.dat

F1 domain of FoF1-ATPase from Bacillus PS3,step waiting,lowATP

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 (7)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. 折叠分类 (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)