8oh5

Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 2)

Method: ELECTRON MICROSCOPY D_max: 291.9 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	8oh5
沉积日期 deposition_date	2023-03-20
结构标题 title	Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 2)
关键词 keywords	flavin based Electron-bifurcation, transhydrogenases, anaerobic metabolism, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	75.81 Å
回转半径 Rg (电子) rg_electron	76.11 Å
零角强度 I(0) i0	10661000000.00
分子量 molecular_weight	848540.0 kDa
排除体积 excluded_volume	1050200 Å³
包络体积 envelope_volume	1654400 Å³
水化壳体积 shell_volume	185210 Å³
包络直径 envelope_diameter	268.3 Å
壳层 Rg shell_rg	74.06 Å
包络 Rg envelope_rg	74.16 Å
形状 Rg shape_rg	76.08 Å
总 Rg total_rg	76.20 Å
总原子数 total_atoms	58624
残基数 n_residues	7624
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	291.9 Å
Rg (实空间) rg_real	80.99 Å
Rg 误差 (实空间) rg_real_error	2.34 Å
I(0) (实空间) i0_real	1.0780e+10
I(0) 误差 (实空间) i0_real_error	2.4560e+08
Rg (倒空间) rg_reciprocal	75.21 Å
I(0) (倒空间) i0_reciprocal	10640000000.0000
解质量估计 total_estimate	0.8479
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	83.4 Å
偏度 Skewness skewness	0.680
峰度 Kurtosis kurtosis	0.257
角度范围 angular_range	— – 0.1050 Å⁻¹
当前正则化参数 α current_alpha	0.9030
最高正则化参数 α highest_alpha	433300000.0000
实空间数据点数 n_real_points	22
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.610; Stabil: 0.837; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.729

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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 (10)

Entity 1 polymer

描述 description	NAD-dependent formate dehydrogenase gamma subunit
分子量 formula_weight	18973.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D,G,J
原子数 atom_count	58624

MCNSCEKELETKFPADKIDLTLLEPVFKEYAGKAGSIIGILQKTQEIYGYLPLAALQAIADNTDNKRAKIYGIATFYSQFRLNPVGKYVILQCQGTACHVLGSKAIGSAICDELGITPGQTTADGLFTLEDVACLGCCSLAPVIMINGEAYGKLTPTSVRKILQDIAEAEKGGVVSEG

Entity 2 polymer

描述 description	NAD-reducing hydrogenase subunit HoxF
分子量 formula_weight	63569.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,E,H,K

MKVRVGLGSCGIAAGGRKVMDRLAQEIKNHGKEIELLPTGCIGMCFYEPIVDVFDGDKVYSYANVTADMATEIFNSHIIGGQPLTQYIVSTTEKPYTILAKQVRIALRNCGVIDPENVDEYKANDGYKALSKALKEMTPEEVIEEIKVAGLRGRGGAGFPTWFKWNAARQSKGEIKYVVCNADEGDPGAFMDRSVLEGDPHALLEGMAICGYAIGANEGHIYCRAEYPLAIKRLEIAIADAKQRNLLGKNIMGTNFSFDMKIKKGAGAFVCGEETALIASLEGERGMPRLKPPFPAQSGFWGKPTNINNVETFANVPWIMYNGGSAYAAYGTEKSKGTKVFALAGKIKNGGLVEVPMGMSLREVIYDIGGGILNDREFKAVQMGGPSGGCIPKQLLDTPVDYDSINKTGAIMGSGGMIVMDETTCMVDMARFFLDFTVKESCGKCIYCRIGTKRMLEILERITTGEGREGDIEELEELSISIKDGSLCGLGQTAPNPVLTTIRYFRDEYEAHIRDKKCPAKSCKPLLTYTINQDNCKGCTLCAQKCPVQAITGEKKKPHVIDQALCTKCGNCASVCRLDAVCIE

Entity 3 polymer

描述 description	Formate dehydrogenase-O, major subunit
分子量 formula_weight	126488.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

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

MSKISININGRELVVSAGQTILQAAAEHGIEIPHLCHDERIQPYGACGLCVVEVEGSPKLVRSCATSVQNGQVIRTDTSRTVVARKTALQLLASDHRGDCRPPCMLACPAQTDCQGYVGLIANGQYEEALKLIKDKMPIPASIGKICPHPCETACRRELVEEPISIAQLKSFVAEVDLNGNQYQPPMKPATGKKVAVVGAGPAGLTAAYFLARDGHKVVIYEAMPHPGGMLRYGIPQYRLDKALLDAEVALMTKMGIEIIYNTKIGDDVSLDYLHDNYDAVFLGIGSWQSQGLRCKGEDMEGVLGGIDFLREVTMNSNITLGGKVLVVGGGNTAMDVARTSKRLGAEEVTIIYRRTIDEMPAEKIEIHEAQEEGVKFQLLVAPVEVLGENGHAKALKCEIMRLGEPDASGRRKPEPTGETVVYEADRIIAAIGQKTVIGNIKDIATDKSGNIIVNGGAFTTNRDKVFAGGDAVTGPKIAIDAIAQGKNAAQVIDSYLNGCLVPHADSQYFTQKDITAADLADRAKAPRVSLTVEDAEVRNKSFMQVAKTFTEEEALRESKRCLECGCRDYFECQLIKYIQDYDVSTEKDSQVECHKTTEFDNHPFIERNPDKCVLCGLCVRVCDEVVGATAIGLVGRGFDSVIMPEFKLPLSETACISCGQCVDVCPTGACMEKQVSYKQIPANMDSMASVCGYCGVGCNVNIEYKGDVVFRVTPDRVNDDGWLCQRGKFGLGHANDKARLTAPVIKRNGQFVKVDWNEANLEVVKRLQAVVAAYGKDSIGVVVSPRLTNEELFLAGKLADAVNTTIKTSYSVDGGSGLGSVLGYDASTNSFAELDNSDFVLTLGKVKENHPVLDFKIRLSGVCSVAWPQSLANTADMKVFLKALLNLGVDENKVAEKTEGFAELKASLADVKVSEEIQALAQKYAKAAKPLIVIDEDTVSAEAVKLMAYAAVITGKIGAAYRGIILVRTKNNTQGAVDMGFVMPVSAVAQGIESGKIKALVVIGEDPAAYPQESALLQKLSFLVVYDMFMTKTATAADMVVPLVSSAEVNGTYTRSDRRIQAVRAAIQPKTGKATLQILIETLKSLGIKYDTIADVRAAIASEVSNYAGMDAADFGTTVYWPNNKNVLYTDGFATEGQKAILAAVGDVPVFVEKKKYDSVEMNFVNGRQSL

Entity 4 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	FLAVIN MONONUCLEOTIDE
分子量 formula_weight	456.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 7 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	36

Entity 8 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 9 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 10 non-polymer

描述 description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	745.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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6. 折叠分类 (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

结构域编号 domain_id	8oh5B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8oh5B02
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	11540 — NADH-ubiquinone oxidoreductase 51kDa subunit

结构域编号 domain_id	8oh5B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	600 —

结构域编号 domain_id	8oh5B04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain

结构域编号 domain_id	8oh5E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8oh5E02
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	11540 — NADH-ubiquinone oxidoreductase 51kDa subunit

结构域编号 domain_id	8oh5E03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	600 —

结构域编号 domain_id	8oh5E04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain

结构域编号 domain_id	8oh5H01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8oh5H02
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	11540 — NADH-ubiquinone oxidoreductase 51kDa subunit

结构域编号 domain_id	8oh5H03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	600 —

结构域编号 domain_id	8oh5H04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain

结构域编号 domain_id	8oh5K01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	8oh5K02
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	11540 — NADH-ubiquinone oxidoreductase 51kDa subunit

结构域编号 domain_id	8oh5K03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	20 — Ubiquitin-like (UB roll)
同源超家族 H-superfamily homologous superfamily	600 —

结构域编号 domain_id	8oh5K04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1440 — de novo design (two linked rop proteins)
同源超家族 H-superfamily homologous superfamily	230 — NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain

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7. 引用文献 (1)

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分辨率 resolution	3.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	54596

fit	/app/data/saxs_computation/oh/8oh5/8oh5.fit
pddf	/app/data/pr_computation/oh/8oh5/8oh5.pr.out
profile	/app/data/saxs_computation/oh/8oh5/8oh5.dat

Cryo-EM structure of the electron bifurcating transhydrogenase StnABC complex from Sporomusa Ovata (state 2)

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 (10)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

6. 折叠分类 (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)