8tpt

nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (long TM6/short TM6)

Method: ELECTRON MICROSCOPY D_max: 121.8 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	8tpt
沉积日期 deposition_date	2023-08-04
结构标题 title	nhTMEM16 A444P mutant in lipid nanodiscs with MSP1E3 scaffold protein in the presence of Ca2+ (long TM6/short TM6)
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	36.88 Å
回转半径 Rg (电子) rg_electron	36.27 Å
零角强度 I(0) i0	210993000.00
分子量 molecular_weight	125780.0 kDa
排除体积 excluded_volume	160800 Å³
包络体积 envelope_volume	215540 Å³
水化壳体积 shell_volume	50462 Å³
包络直径 envelope_diameter	121.0 Å
壳层 Rg shell_rg	41.81 Å
包络 Rg envelope_rg	35.74 Å
形状 Rg shape_rg	36.27 Å
总 Rg total_rg	36.68 Å
总原子数 total_atoms	8908
残基数 n_residues	1150
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	121.8 Å
Rg (实空间) rg_real	36.87 Å
Rg 误差 (实空间) rg_real_error	1.32 Å
I(0) (实空间) i0_real	2.1100e+08
I(0) 误差 (实空间) i0_real_error	4.1830e+06
Rg (倒空间) rg_reciprocal	36.88 Å
I(0) (倒空间) i0_reciprocal	211000000.0000
解质量估计 total_estimate	0.8905
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	39.7 Å
偏度 Skewness skewness	0.298
峰度 Kurtosis kurtosis	-0.462
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	32580000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.872

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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 (3)

Entity 1 polymer

描述 description	Lipid scramblase nhTMEM16
分子量 formula_weight	83320.1 kDa
突变 mutation	A444P
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	8908

GPSNLKDFSQPGSGQESNFGVDFVIHYKVPAAERDEAEAGFVQLIRALTTVGLATEVRHGENESLLVFVKVASPDLFAKQVYRARLGDWLHGVRVSAPHNDIAQALQDEPVVEAERLRLIYLMITKPHNEGGAGVTPTNAKWKHVESIFPLHSHSFNKEWIKKWSSKYTLEQTDIDNIRDKFGESVAFYFAFLRSYFRFLVIPSAFGFGAWLLLGQFSYLYALLCGLWSVVFFEYWKKQEVDLAVQWGVRGVSSIQQSRPEFEWEHEAEDPITGEPVKVYPPMKRVKTQLLQIPFALACVVALGALIVTCNSLEVFINEVYSGPGKQYLGFLPTIFLVIGTPTISGVLMGAAEKLNAMENYATVDAHDAALIQKQFVLNFMTSYMALFFTAFVYIPFGHILHPFLNFWRATAQTLTFSEKELPTREFQINPARISNQMFYFTVTPQIVNFATEVVVPYIKQQAFQKAKQLKSGSKVQEDHEEEAEFLQRVREECTLEEYDVSGDYREMVMQFGYVAMFSVAWPLAACCFLVNNWVELRSDALKIAISSRRPIPWRTDSIGPWLTALSFLSWLGSITSSAIVYLCSNSKNGTQGEASPLKAWGLLLSILFAEHFYLVVQLAVRFVLSKLDSPGLQKERKERFQTKKRLLQENLGQDAAEEAAAPGIEHSEKITREALEEEARQASIRGHGTPEEMFWQRQRGMQETIEIGRRMIEQQLAAGKNGKKSAPAVPSEKASA

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

Entity 3 non-polymer

描述 description	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
分子量 formula_weight	749.0 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	3.01 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	84643

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