9h1l

Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP

Method: ELECTRON MICROSCOPY D_max: 166.3 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	9h1l
沉积日期 deposition_date	2024-10-09
结构标题 title	Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP
关键词 keywords	Methyl-coenzyme M reductase, activation complex, ATPase, Iron-sulfur clusters, OXIDOREDUCTASE; OXIDOREDUCTASE
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	50.14 Å
回转半径 Rg (电子) rg_electron	50.12 Å
零角强度 I(0) i0	3093040000.00
分子量 molecular_weight	464510.0 kDa
排除体积 excluded_volume	580420 Å³
包络体积 envelope_volume	728470 Å³
水化壳体积 shell_volume	115640 Å³
包络直径 envelope_diameter	171.5 Å
壳层 Rg shell_rg	57.10 Å
包络 Rg envelope_rg	50.21 Å
形状 Rg shape_rg	50.15 Å
总 Rg total_rg	50.22 Å
总原子数 total_atoms	32524
残基数 n_residues	4133
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	166.3 Å
Rg (实空间) rg_real	50.07 Å
Rg 误差 (实空间) rg_real_error	1.51 Å
I(0) (实空间) i0_real	3.0930e+09
I(0) 误差 (实空间) i0_real_error	5.8170e+07
Rg (倒空间) rg_reciprocal	50.18 Å
I(0) (倒空间) i0_reciprocal	3093000000.0000
解质量估计 total_estimate	0.8738
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	59.0 Å
偏度 Skewness skewness	0.320
峰度 Kurtosis kurtosis	-0.323
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	429700000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.800

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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 (17)

Entity 1 polymer

描述 description	UPF0288 protein MmarC6_0796
分子量 formula_weight	56520.8 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	J
原子数 atom_count	32524

MNVLVNNNPKSGKTLEDVIKDEYYIPGSNIVIIKGTATVIKEETKKYLIKTTKGSFVVGITEENETVDFWNKNYKSFEDKSLIWKSISDVSFGSIEIPLPVSSVKQNFKKWDVVLSVSGLDTSEGNLIFVQRDVLELYGLENPKIGILIGGKRVLKTLTADDRIISIEQMRESKENIDYEITTNLNKEIQDTWKIYTYCKAEFDGPPQSTEHALAILENGTLEISENTNTYVADCRLQTLFIDEENPEDRDRGTITVRNIGNGVGKVYIYQESRASSLSHTVVGKVTDGIEIVDFSNSGHITVKTNPERLSVIGKTQKDAKILFEKHGITLKMEGNIDEDAIIVEQVPEYTMDILKSKEVTTKGIEPEKLLYVEIYDKDAPTTSWYFRKVTGLTTKRIGTLKIYFKHDDISMFERDWDYSKGLLPENTPEKSIDSGIIAVTNMVKKYKGYIGVRTSSNDKYGPTGETFEGTNIVGKVVKNSEILKSVKQGENIYILEVNSN

Entity 2 polymer

描述 description	Methyl-coenzyme M reductase subunit gamma
分子量 formula_weight	29665.5 kDa
EC 编号 ec_number	2.8.4.1
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B

MAYTPQFYPGATKVAENRRNHLNPNYELEKLREIPDEDVVKIMGHRQPGEDYKTVHPPLEEMDFVEDYARDLVEPLNGAKEGHRVRYIQFADSMYFAPAQPYDRSRSYMSRLRGVDAGTLSGRQVVECRESDLEEFSKNILMDTELFDPATSGMRGATVHGHSLRLDENGMMFDALQRCVFDEKTGHVMYVKDQVGKPLDAPVDVGEPIPEAKLREITTIYRNDGVAMRADPDVIEVVKRIHRARTLGGYIPTNETFKGL

Entity 3 polymer

描述 description	Methyl-coenzyme M reductase subunit beta
分子量 formula_weight	46701.2 kDa
EC 编号 ec_number	2.8.4.1
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MVKYEDKISLYDAKGNLVAENVPLEAISPLYNPTIKSMVKNIKRTVAVNLAGIEGTLAAGKIGGKGCQVPGRTLDISAVSNAQAIADEVEKILKVSEDDDTAVKIINGGKQLAVQVPTARLEVAAEYSVSMLSTAMALKEALIKTFNIDMFDGSTVHAAIVGNYPQVMDYAGGNIASLLGAPSMMEGLGYALRNIPVNHAVATTKKNMMNAIAFSSVMEQTATFEMGDAVGSFERQHLLGLAYQGLNADNLVIDFIKANAKGTVGSVVETVIDRAIADGVIVVDKTMSSGFNMYKPADVNKWNAYAAAGLVAAVAVSCGAARAAQNVASVILYFNDILEYETGLPGVDYGRSMGTAVGFSFFSHSIYGGGGPGIFNGNHVVTRHSKGFAIPPVCAAMCADAGTQMFSPEHTSGLVGSVYSAFDEFREPMKYVIEGALSIKDQF

Entity 4 polymer

描述 description	Methyl-coenzyme M reductase subunit alpha
分子量 formula_weight	61230.7 kDa
EC 编号 ec_number	2.8.4.1
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MEAEKRLFLKALKEKFEEDPKEKYTKFYTFGGWEQSARKREFVEANEKIVSEKRQGIPLYNPDIGVPLGQRKLMPYKLSNTDDYCEGDDLHFLNNAAIQQLWDDIRRTVIVGMDTAHSVLEKRLGVEVTPETINEYMHTINHSLPGGAVVQEHMVEVHPSLAWDCYARIFTGDDELADELDSRFLIDINKLFPEEQAETLKAAIGKKTYQVSRVPSLVGRVCDGGTISRWSAMQIGMSFITAYKLCAGEAATADFSYASKHADVIQMGNALPGRRARGPNEPGGIRFGILSDVVQTTRVSEDPVEQSLEVVATGAALYDQIWLGAYMSGGIGFTQYATASYTDDILDDFSYYALDYVEKKYGRMGTKATMDVVEDVAGEVTLYALEQYDDYPALLEDHFGGSQRAAVAAAASGIGVCMATGNSNAGVNGWYLSQILHKEYHSRLGFYGYDLQDQCGASNSLAIRNDEAAPLELRGPNYPNYAMNVGHQGEYAGIAQAAHSARGDAFALNPLVKVAFADPMLVFDFSKPRKEIARGALREFEAAGERDVILPAK

Entity 5 polymer

描述 description	Methanogenesis marker protein 17
分子量 formula_weight	21119.5 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	G

MAYIDVECNDEAGKAIYERIIQTSLEDLVLGKSIIKAKMICKQDVPYFIIGILPKSTSKLIRLRDIATIDESKKSDGKTITKLNIDDETYATELLAKINVMDQPSRFEVVTDSEVDLNMVIHDAKEDFIDRVLDFMNRVFPEGMRIRKTIRDKTIVMVASEKPIEEEWMNEAVKLQEELKIFK

Entity 6 polymer

描述 description	Methanogenesis marker protein 7
分子量 formula_weight	35024.7 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

MYQIIRYEGGVYKNNILKEWIEDVGGFIIQEHVMQLDVYMTIAIPQNEIENFKEEAKKYKGKIVETPLAGIEIAIVSPSLSRHHLPHIACDVSEYVRKFGAKPNMIGLAHGAGKNISEIREKEKRLIQEHDIAIYVMGNFESCILDKTHLFKVDIPLVVTGGPETLDIPYTYVGNLGRRAQRLRKGEEIRALRQMIDEVTKKINDKRMELSYDPPIIPPVVLKDEIEKRIDEVRGILAPMPIVTQLDGLRIKMDYDRNHEEIENVKIGKYLLKDIAYVTRSEMKNYILIKLKSTSELKTDENKA

Entity 7 polymer

描述 description	Methyl-coenzyme M reductase operon protein C
分子量 formula_weight	24906.7 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	I

MSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKSAGSGMPVGRKEQIVDCRAVMGLGEGGGLAQRGTFAEGLRNDVVVVAMSPGRRHITKPVCEITYGIREAGIQTSVLVLDAGGGIPSDAPQGSLGSTFGLKPEEAKQVNRHKLCVIHFGNVKSHIIYKARLFLKYVDIPTIIVCQTPVDMEDFAAIGIKTKNVMPLESKTEGKIVEIITGVIRGESAPQKKIDEIIESIKKHLG

来源 Source

来源生物 organism	Methanococcus maripaludis
NCBI 分类编号 ncbi_taxonomy_id	39152
宿主生物 host_organism	Methanococcus maripaludis

Entity 8 polymer

描述 description	Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA
分子量 formula_weight	59572.6 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	K

MLLLEVKNVSKSYGDTEVLKNVSFELNEGDVMGVLGRSGAGKSVLLHMLRGMEGYEPTSGQIIYHVAYCPHCENVEAPSQVGKKCECETEYVAKSVDFWNNNEITYALKKKIAIMLQRTFALYGEKTVAENIMEALTAAGYEGKDATEWALNLIKMVKLEHRVAHISRDLSGGEKQRVVLARQIAKNPVIFLADEPTGTLDPKTAKFVHNALTEAVIKHNIAMVITSHWPEVIEELCQKAIWLDKGEMRLVGESKHVVEEFMKTVTSMKEFEKVEVKDELLKLENVEKRYVSVDRGIVKAVDGIDVSINEKEIFGLVGVSGAGKTTLSKIIAAVIPPSKGNYEFRLADEWVDMTKVGPLYRGRAKRYIGMLFQEYSLYPHRTILYNLTESIGLEMPGEFAKMKAEHTLVSVGFTEEEAENMLEKHPSELSVGEKHRVALAQVLIREPHLILLDEPTGTMDPITRNQVAESIQKSRSELDQTYVIVSHDMDFVLNVCDRAALVRGGKIIKTGKPDEIVKILSEEEKDEMIGH

Entity 9 polymer

描述 description	DUF2098 domain-containing protein
分子量 formula_weight	10640.8 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	L

MTLDRNGKLIEIGSYVRYINTGTHGTVKAIEPKNDEEWVLLENDIYYRPELLELVERRKIEKKESEEELIERITNEDIDLEAAENGCGCSGAG

Entity 10 non-polymer

描述 description	FACTOR 430
分子量 formula_weight	906.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 11 non-polymer

描述 description	1-THIOETHANESULFONIC ACID
分子量 formula_weight	142.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 non-polymer

描述 description	Coenzyme B
分子量 formula_weight	343.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 13 non-polymer

描述 description	O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE
分子量 formula_weight	481.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 14 non-polymer

描述 description	FeFe cofactor
分子量 formula_weight	747.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 15 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	1

Entity 16 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	2

Entity 17 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	2

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7. 引用文献 (1)

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分辨率 resolution	2.14 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	118247

fit	/app/data/saxs_computation/h1/9h1l/9h1l.fit
pddf	/app/data/pr_computation/h1/9h1l/9h1l.pr.out
profile	/app/data/saxs_computation/h1/9h1l/9h1l.dat

Methyl-coenzyme M reductase activation complex binding to the A2 component after incubation with ATP

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 (17)

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

来源 Source

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

Entity 14 non-polymer

Entity 15 non-polymer

Entity 16 non-polymer

Entity 17 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)