9mqx

Electron-bifurcating Tungstopyranopterin-containing aldehyde oxidoreductase with NADH

Method: ELECTRON MICROSCOPY D_max: 203.0 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9mqx
沉积日期 deposition_date	2025-01-06
结构标题 title	Electron-bifurcating Tungstopyranopterin-containing aldehyde oxidoreductase with NADH
关键词 keywords	electron bifurcation, OXIDOREDUCTASE; OXIDOREDUCTASE
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	58.41 Å
回转半径 Rg (电子) rg_electron	59.20 Å
零角强度 I(0) i0	2085230000.00
分子量 molecular_weight	369290.0 kDa
排除体积 excluded_volume	455410 Å³
包络体积 envelope_volume	602170 Å³
水化壳体积 shell_volume	86748 Å³
包络直径 envelope_diameter	209.3 Å
壳层 Rg shell_rg	57.95 Å
包络 Rg envelope_rg	58.78 Å
形状 Rg shape_rg	59.38 Å
总 Rg total_rg	58.58 Å
总原子数 total_atoms	25410
残基数 n_residues	3292
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	203.0 Å
Rg (实空间) rg_real	58.61 Å
Rg 误差 (实空间) rg_real_error	2.17 Å
I(0) (实空间) i0_real	2.0850e+09
I(0) 误差 (实空间) i0_real_error	4.2680e+07
Rg (倒空间) rg_reciprocal	58.21 Å
I(0) (倒空间) i0_reciprocal	2084000000.0000
解质量估计 total_estimate	0.8539
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	75.2 Å
偏度 Skewness skewness	0.309
峰度 Kurtosis kurtosis	-0.536
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	70330000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.874; Smooth: 0.699

▶

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

▶

5. 实体与聚合体信息 (12)

Entity 1 polymer

描述 description	NADH:ubiquinone oxidoreductase chain G-like protein
分子量 formula_weight	27662.2 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	A
原子数 atom_count	25410

MRDPIDIVIDGVSLSVPMETTVLEAAQMAGVEIPTLCHHPALPPDGNCRLCMVEILRPGRRGELAISCMYPIRAQIEVNTKSDEVIRARKFVLKLLLNRAPKSARLNALANEYGVSVESRFSFDPDECVRCDRCVRACETLGPSAIGPAWRGFNKRIVPPFMEPPRQCIGCGACADVCPTGYIECVDEGDERTIWDRKFTLIRCPICGQTYTTEEALKFTGIEDPDARLCPTCRKREYASKFRIFVH

Entity 2 polymer

描述 description	NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit
分子量 formula_weight	67862.2 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	B

MPLFLKPDDLRNYRLKLKDDLKRASLLPVVRVCCGTGCVSNGSMEVLSALEEALKGIGKVEPVVKFTGCHGFCERGPIVIVSPGEIFYQNVKTKDVPEIVQKTILDGEVIERLLYRDPVTKKTYRSDHEIPFYANQQRLVLRRSGHIDPTSIEDYIATDGYEALCLAFKLGPDEIIKQITDSYLRGRGGGGFRTGYKWKSCREVDDFPKYVIANGDEGDPGAFMDRSLMEGDPHSVIEGMIIGAYAIGANEGYIYVRNEYPLAVRRLQIAIERAREYGLLGKNILGSGFDFDIQICKGGGAFVCGESSALMRSIEGYPGVPRVKYIHATEQGLWDKPTVLNNVETWANVPIILMNGVEWYKSLGTERNSGTKIFALVGKVKNTGLVEVPMGVTLRKIIYEIGGGTLKDKAFKAVQTGGPSGGCIPASLLDLSVDFDTLVKAGSMMGSGGMIVMDERSCMVDVAKYFIDFLVEESCGKCTPCREGLKVLQKLLHDLTEGKGSLQDVGLLEDTAHELGKTALCGLGKTAANPVLSTLKYFHEEYEEHVEGYCRAGVCTGLFAAKIDKDSCIGCGQCARTCPVKAISGEVRGPHVVDALKCIGCGQCMDVCPTNSIASSRRVKNA

Entity 3 polymer

描述 description	NADH:ubiquinone oxidoreductase 24 kD subunit
分子量 formula_weight	17547.5 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	C

ATSDVAISDILCRYEKNPRFLLQVLLDVQEKFRYLPTDAMRSVAEYFEIPESRVFAVATFYKVLSLVPKGEKTIKVCQGTACHLRGGSQILNAISERLKIRAGETTKDGIFTLETVNCLGCCAMAPVMMVGDKVYGKLSVADVARILEAEKEDAIISKA

Entity 4 polymer

描述 description	Aldehyde:ferredoxin oxidoreductase
分子量 formula_weight	65158.6 kDa
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,F,H

MFGYMGKVLRVNLSTKNITLEPLRMDWAKDFLGARGLGSRYLVEEVDPNVDPFSPDNKLIFATGPVTGTLATSAGRFNVVTKGPLTGTIAASNSGGYFGPELKYAGYDMIIFEGKSANPVYLWIYNDHVELRDASHVWGKDSYETTDALLSETDPEAKVACIGPAGERLVLFACVMNDKHRAAGRTGVGAVMGSKNLKAVVVRGTGGIKLADKEAFLEALRKARKKIAEHPVTGGGLPAYGTNVLVNVINAAGALPTRNFKEAWFEGADKISGETMAETILLKNKACASCASACGRVTKAMGEIGEGPEYEAVWAYGAQCGVDNLEAICKANFICNKLGMDPITMGSTIGCAMELAELGLIDEKKAGVSLHWGNAEAIVKLTEDTGYRRGFGEELALGSYRLGEKYGHPELSMSAKKQEMPAYDPRALQGMGLEYATSNRGGCHVRGYLTSPEVLGIPEKLDPTDIASKPQWTKTFQDLTAAVDSLGFCLFLTFALDAGDLAAQVAPIIGREVTAEELLLAGERIWNLERLFNLKAGISPKEDTLPPRLLNEPIPAGPSKGRVNKLHEMLPKYYELRGWGKNGIPTKERLESLGLLDIAAKYSL

Entity 5 polymer

描述 description	Fe-S-cluster-containing hydrogenase subunit
分子量 formula_weight	16593.3 kDa
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	E,G,I

MEKVLVISPEKCVGCGSCELACSLEKEGECRPSLARVTVYRFEAGANVPMTCQQCDDAPCISVCKAGALARDEKNVVQVDSSKCIGCRMCVMACPFGNMSYHWEQSTAIKCDQCNGSPYCVEFCPTKALDYVPADAISLQKKKEFSARFAKI

Entity 6 non-polymer

描述 description	IRON/SULFUR CLUSTER
分子量 formula_weight	351.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	20

Entity 7 non-polymer

描述 description	FE2/S2 (INORGANIC) CLUSTER
分子量 formula_weight	175.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

Entity 8 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

Entity 9 non-polymer

描述 description	FLAVIN MONONUCLEOTIDE
分子量 formula_weight	456.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 10 non-polymer

描述 description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
分子量 formula_weight	665.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 11 non-polymer

描述 description	TUNGSTOPTERIN COFACTOR
分子量 formula_weight	1024.8 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

Entity 12 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

▶

7. 引用文献 (1)

▶

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

分辨率 resolution	3.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	737000

fit	/app/data/saxs_computation/mq/9mqx/9mqx.fit
pddf	/app/data/pr_computation/mq/9mqx/9mqx.pr.out
profile	/app/data/saxs_computation/mq/9mqx/9mqx.dat

Electron-bifurcating Tungstopyranopterin-containing aldehyde oxidoreductase with NADH

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

精修参数 Refinement

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 non-polymer

Entity 7 non-polymer

Entity 8 non-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)