8rvu

CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2 (composite structure)

Method: ELECTRON MICROSCOPY D_max: 189.4 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	8rvu
沉积日期 deposition_date	2024-02-02
结构标题 title	CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2 (composite structure)
关键词 keywords	Redox, Flavin-based electron bifurcation, methanogenesis, heterodisulfide reductase, F420-H2 oxidase, 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	52.60 Å
回转半径 Rg (电子) rg_electron	53.02 Å
零角强度 I(0) i0	1653880000.00
分子量 molecular_weight	325560.0 kDa
排除体积 excluded_volume	400680 Å³
包络体积 envelope_volume	533250 Å³
水化壳体积 shell_volume	84721 Å³
包络直径 envelope_diameter	189.2 Å
壳层 Rg shell_rg	54.59 Å
包络 Rg envelope_rg	52.87 Å
形状 Rg shape_rg	53.14 Å
总 Rg total_rg	52.65 Å
总原子数 total_atoms	44199
残基数 n_residues	2853
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	189.4 Å
Rg (实空间) rg_real	52.80 Å
Rg 误差 (实空间) rg_real_error	2.52 Å
I(0) (实空间) i0_real	1.6540e+09
I(0) 误差 (实空间) i0_real_error	3.7040e+07
Rg (倒空间) rg_reciprocal	52.42 Å
I(0) (倒空间) i0_reciprocal	1653000000.0000
解质量估计 total_estimate	0.8467
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	63.1 Å
偏度 Skewness skewness	0.473
峰度 Kurtosis kurtosis	-0.151
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	79060000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.750

▶

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

▶

5. 实体与聚合体信息 (11)

Entity 1 polymer

描述 description	Formate dehydrogenase, beta subunit
分子量 formula_weight	43387.1 kDa
EC 编号 ec_number	1.2.1.2
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	E
原子数 atom_count	44370

MKYLLARATDEEIQRKGECGGAVTAIFKYMLDKEVVDAVLTLERGYDVYDGIPVLLEDSSGIESTCGSLHCAPTMFGDLISRYLSDMRLAVAVKPCDAMAIRELEKRHQIDPDKVYKIGLNCGGTLAPVSAREMIETFYEIDPDDVVSEEIDRGKFIVELRDGSHREISIDYLEEEGFGRRENCQRCEIMVPRNADLACGNWGADDGWTFIEVNTERGQEIIEGARSSGYIEAREPSEKMVKIREKIENAMISMARKFQDKYLDEEYPSLDEWDEYWKRCINCFACRDACPVCFCRECELEKDYLLESDEKAPDPLTFQGVRLSHMGFSCINCGQCEDVCPMDIPIARIYHRIQKKYRDRTGFTAGVSQELPPMYSGEKD

Entity 2 polymer

描述 description	Formate dehydrogenase, alpha subunit
分子量 formula_weight	37682.7 kDa
EC 编号 ec_number	1.2.1.2
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

MMVKHTLCPSCSAGCGVNIVEMGGAPVGTYPYRRHPVNEGKTCRAGRDCYEIPLMDRVTSPGVKKSGKLSGVNWDEALDKLTELLSSEDISILTTGTLTNEEALKLREIIENFNVKKSGLITVFPEFDYPEIDIRNIRDYDNIAVIGDAITCAPLIGRRIFHAMAAGAEVRSYDRRDETRMAVNSGFHITFSDEREVLNDLQQLPGGSLIIITPEIPEIIGPVLEFSSENEFDVLPIFEDFNTRGVMQHLPPVNEGEFDSVWLIDPGAAAEPVDVSGKFVLQSIRTEGLTPDIFLPVAAWCEKSGSYTSTAGYTMKLEPALQAPEGVLSDMEIFERILRAGD

Entity 3 polymer

描述 description	Methyl viologen-reducing hydrogenase, subunit D-related protein
分子量 formula_weight	15550.8 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	F

MSFEPKIVGFCCNWCSYGGADTAGTARMQYPPNVRIIRVMCSGRVNASMILKAFSEGADGVFVGGCHIGDCHYDSGNYKWKRRARFIEDILPEFGIDKERFRWEWISASEGEKFQKTMQEFYETVKYLGPLKRAGK

Entity 4 polymer

描述 description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit B
分子量 formula_weight	33496.4 kDa
EC 编号 ec_number	1.8.98.5
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	b,B

MEIAYFLGCIMNNRYPGIEKATRVLFDKLGIELKDMEGASCCPAPGVFGSFDKTTWAAIAARNITIAEDMGADIMTECNGCFGSLFETNHLLKEDEEMKAKINEILKETGREYKGEVNVRHFAEVLYNDVGLDKLSELVEKPLNLNVAVHYGCHFLKPSDEINIDNPERPTILDEIVEVTGAKSVEYKDKMMCCGAGGGVRSRDLDVALDFTREKLTNMKEAGVDAIVNVCPFCHLQFDVGQMEIKDKFGEEFDIPVLHLAQLLGLAMGLPKEDLVVDAHQVCVDECLEKLEELDRLAPGSG

Entity 5 polymer

描述 description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit C
分子量 formula_weight	20548.7 kDa
EC 编号 ec_number	1.8.98.5
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,C

MTLLQREENIIRKGNIDKEFSEKIKAAGGDSLEYCFQCGTCTGSCPSGRRTPYRVRQIIRKANVGLKDEIISDPTLWMCTTCYSCQERCPRKVKIVDVVKLARNEAAKAGFMAPAHKAVGSFVIKTGHGVPINDATMELRKAVGLGELPPTTHQFPEALEEVQKIIKATGFDQLIGYNWETGELE

Entity 6 polymer

描述 description	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A
分子量 formula_weight	72265.0 kDa
EC 编号 ec_number	1.8.98.5
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,A

MAEEKKETMEEPKIGVYVCHCGVNIGGVVDVEAVRDYAAKLPNVVIAKDYKYYCSDPGQLEIQKDIKELGINRVVVAACSPRLHEPTFRRCVEEAGLNQFLFEFANIREHDSWVHMDNPEGATEKAKDLVRMAVAKARLLEPLEASKVSVDDKALVIGGGVAGIQAALDLADMGFKTYMVEKRPSISGRMGQLDKTFPTLDCSMCILAPKMVDVGKHDNIELITYAEVKEVDGYIGNFKVKIEKKPRYIDEELCTGCGSCVEVCPIEMPNYFDEGIGMTKAVYIPFPQAVPLCATIDKDYCIECMLCDEVCERGAVKHDQEPEEIEIEVGTIIVATGYDAYDPTEKLEYGYGRHTNVITGLELERMINASGPTDGKVLKPSDGEKPKRVAFIHCVGSRDEQIGKPYCSRVCCMYIMKNAQLIKDKMPDTEVTLYYMDIRAFGKGFEEFYKRSQEKYGIKFIRGRPAEVIENPDLTLTVRSEDTLLGKVTEYDYDMVVLGVGLVPPEGAETLRQTIGLSKSADGFLMEAHPKLRPVDTLTDGVYLAGVAQGPKDIPDAVAQASGAAARAAIPMVKGEVEIEPIIAVTDSDVCGGCEVCIELCPFGAISIEEGHANVNVALCKGCGTCVAACPSGAMDQQHFKTEQIMAQIEAALNEPASK

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	18

Entity 8 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	3

Entity 9 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	1

Entity 10 non-polymer

描述 description	Non-cubane [4Fe-4S]-cluster
分子量 formula_weight	351.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

Entity 11 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	171

▶

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	2.22 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	234858

fit	/app/data/saxs_computation/rv/8rvu/8rvu.fit
pddf	/app/data/pr_computation/rv/8rvu/8rvu.pr.out
profile	/app/data/saxs_computation/rv/8rvu/8rvu.dat

CryoEM structure of the Elp-Hdr complex of Methanothermobacter marburgensis state 2 (composite structure)

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 (11)

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 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)