SAXSdb — 9jje

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9jje
沉积日期 deposition_date	2024-09-13
结构标题 title	Nematostella vectensis TRPM2 tetramer in complex with ADPRP/Ca2+
关键词 keywords	Nematostella vectensis, TRPM2, ADPRP, Ca2+, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	50.08 Å
回转半径 Rg (电子) rg_electron	49.81 Å
零角强度 I(0) i0	2410890000.00
分子量 molecular_weight	432710.0 kDa
排除体积 excluded_volume	550190 Å³
包络体积 envelope_volume	768960 Å³
水化壳体积 shell_volume	122530 Å³
包络直径 envelope_diameter	160.4 Å
壳层 Rg shell_rg	58.76 Å
包络 Rg envelope_rg	48.31 Å
形状 Rg shape_rg	49.82 Å
总 Rg total_rg	50.06 Å
总原子数 total_atoms	30472
残基数 n_residues	3764
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	156.5 Å
Rg (实空间) rg_real	49.83 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	2.4110e+09
I(0) 误差 (实空间) i0_real_error	3.9320e+07
Rg (倒空间) rg_reciprocal	50.28 Å
I(0) (倒空间) i0_reciprocal	2412000000.0000
解质量估计 total_estimate	0.8807
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	65.6 Å
偏度 Skewness skewness	0.088
峰度 Kurtosis kurtosis	-0.450
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	272800000.0000
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: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.854

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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 (4)

Entity 1 polymer

描述 description	Transient receptor potential cation channel subfamily M member-like 2
分子量 formula_weight	176663.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	30472

MGKDSFTPLYDGGDSSHVHLNKFGSNQLSQSKKSWIARNFSRRECIRFVPKSHDVSRCKCGRPRERHSQQALESGQGSEEWNVASCTTKHPTNAYGEIDFEGYGGQKRAPYLRMSHDTDANLVITLMLKRWNLEIPNLVISVTGGAKSFVLKPRLREMFRRGLIKAAKTTGAWIITGGTNTGVMKHVGEAVKEQQLMFGSDTQVNVIGIATWGIVDKQSDLISEKNGKYPALYSMEPTPGHQGAMLDPNHSHFFLVDDGTEGKYGVEIGMRSRIEEAIMKVKTDSRSEAGSIGVPVVLLVLEGGPNTVATMYELIKKKVPAVVIDGSGRAASVVGFAYNHTIKRNVDGQTINVIDPQYEDEVRAKVVEVFGAKGADKTYSMIKDVLEDEKMISVYSLDGEISQDIDLAILKALLKANRSSPVAQLNLALAWNRIDLAKSDIFTEEQQWTTETLSAAMLTALLDDKAEFAELFLQNGLSMREFLSLDILCKLYAEVPGNTTIKPLLQKEMGKRQVKTIDMDVVGEVIEELMGDMFESYYRKDGHYFGELASYAEGLVLKNRKSSKDLLANINRIDPLPTPYLDVFLWAVLCNRRELARVLWEAGREPMAAALMASRLLKRMASRAQEDNTITDISSDLYDHARLFEERAVGVLDECFNENETLSQTLLVRELDHYSRMTALELAVSAESQDFIAHTSCQVLLTRLWMGTMAMNTRWWKVLVCLYLPVLIFPIIYFVPDEQHERQAAEREHQKSLNQKSSKVKSHKEKNDAPVVPVYRSKEEKAVSNDEEARVGTENEEEDFQLEDYIPEIREDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEIQGEKPKEFGEVDPDGRWLSPLLLAIYMVFTNILLLNLLIAIFNYTFERVQEDSDKVWKFQRYDLVQEYHSRPVFAPPLVLLGHILIFIRWVWRMCRCGHPPRGSTMKIGLSPAEMEQMDNWEFQAAEMYIHQQQQKNSGTLEERVRALGDRVDCINSQLNRVLDSMSGTRAHALTDGNGLEGGHDSEGRLARMEVELSSNSESLQKILALLQQQPPVKGQAAVPIQLTLLHYKARSSPYPGSTAKRFAVQDNMVDWQVPFPDYKPVNYTAPVVLANPVWADKDLMAMSPRPELPYNQMDHTCNVNRVSYNGTYVVKDGLPLNPMGRTGMQGRGLLGRFGPNHAADPVVTRWKRTSAGVMLQGGKKVLEFVAIQRKDNNQWAIPGGMVEPGQLVTQALKAEFGEEAMAKLNVSQEEKERIAKQIERLFQQGQEIYKGYVDDPRNTDNAWMETVAVNFHDDKGDLFGDITLQAGDDAAAVRWQRVSGNIPLYASHVSILEKVAKMRDAAFSNSLEVLFQ

来源 Source

来源生物 organism	Nematostella vectensis
通用名 common_name	starlet sea anemone
NCBI 分类编号 ncbi_taxonomy_id	45351
宿主生物 host_organism	Homo sapiens

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 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 4 non-polymer

描述 description	;[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE ;
分子量 formula_weight	639.3 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	2.52 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	377471

fit	/app/data/saxs_computation/jj/9jje/9jje.fit
pddf	/app/data/pr_computation/jj/9jje/9jje.pr.out
profile	/app/data/saxs_computation/jj/9jje/9jje.dat

Nematostella vectensis TRPM2 tetramer in complex with ADPRP/Ca2+

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