8tpn

nhTMEM16 lipid scramblase in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+ (intermediate state)

Method: ELECTRON MICROSCOPY D_max: 125.0 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8tpn
沉积日期 deposition_date	2023-08-04
结构标题 title	nhTMEM16 lipid scramblase in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+ (intermediate state)
关键词 keywords	membrane protein, lipid scramblase, TMEM16, LIPID TRANSPORT; LIPID 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	38.11 Å
回转半径 Rg (电子) rg_electron	37.32 Å
零角强度 I(0) i0	199938000.00
分子量 molecular_weight	121660.0 kDa
排除体积 excluded_volume	155330 Å³
包络体积 envelope_volume	224560 Å³
水化壳体积 shell_volume	50783 Å³
包络直径 envelope_diameter	127.4 Å
壳层 Rg shell_rg	43.11 Å
包络 Rg envelope_rg	36.59 Å
形状 Rg shape_rg	37.31 Å
总 Rg total_rg	37.79 Å
总原子数 total_atoms	8612
残基数 n_residues	1102
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	125.0 Å
Rg (实空间) rg_real	38.10 Å
Rg 误差 (实空间) rg_real_error	1.08 Å
I(0) (实空间) i0_real	1.9990e+08
I(0) 误差 (实空间) i0_real_error	3.1150e+06
Rg (倒空间) rg_reciprocal	38.11 Å
I(0) (倒空间) i0_reciprocal	199900000.0000
解质量估计 total_estimate	0.8896
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	39.6 Å
偏度 Skewness skewness	0.275
峰度 Kurtosis kurtosis	-0.511
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31780000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.813

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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 (2)

Entity 1 polymer

描述 description	Lipid scramblase nhTMEM16
分子量 formula_weight	83294.1 kDa
来源方法 src_method	man
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
原子数 atom_count	8612

GPSNLKDFSQPGSGQESNFGVDFVIHYKVPAAERDEAEAGFVQLIRALTTVGLATEVRHGENESLLVFVKVASPDLFAKQVYRARLGDWLHGVRVSAPHNDIAQALQDEPVVEAERLRLIYLMITKPHNEGGAGVTPTNAKWKHVESIFPLHSHSFNKEWIKKWSSKYTLEQTDIDNIRDKFGESVAFYFAFLRSYFRFLVIPSAFGFGAWLLLGQFSYLYALLCGLWSVVFFEYWKKQEVDLAVQWGVRGVSSIQQSRPEFEWEHEAEDPITGEPVKVYPPMKRVKTQLLQIPFALACVVALGALIVTCNSLEVFINEVYSGPGKQYLGFLPTIFLVIGTPTISGVLMGAAEKLNAMENYATVDAHDAALIQKQFVLNFMTSYMALFFTAFVYIPFGHILHPFLNFWRATAQTLTFSEKELPTREFQINPARISNQMFYFTVTAQIVNFATEVVVPYIKQQAFQKAKQLKSGSKVQEDHEEEAEFLQRVREECTLEEYDVSGDYREMVMQFGYVAMFSVAWPLAACCFLVNNWVELRSDALKIAISSRRPIPWRTDSIGPWLTALSFLSWLGSITSSAIVYLCSNSKNGTQGEASPLKAWGLLLSILFAEHFYLVVQLAVRFVLSKLDSPGLQKERKERFQTKKRLLQENLGQDAAEEAAAPGIEHSEKITREALEEEARQASIRGHGTPEEMFWQRQRGMQETIEIGRRMIEQQLAAGKNGKKSAPAVPSEKASA

来源 Source

来源生物 organism	Fusarium vanettenii 77-13-4
NCBI 分类编号 ncbi_taxonomy_id	660122
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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7. 引用文献 (1)

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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	4.07 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	61965

fit	/app/data/saxs_computation/tp/8tpn/8tpn.fit
pddf	/app/data/pr_computation/tp/8tpn/8tpn.pr.out
profile	/app/data/saxs_computation/tp/8tpn/8tpn.dat

nhTMEM16 lipid scramblase in lipid nanodiscs with MSP2N2 scaffold protein in the presence of Ca2+ (intermediate state)

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)