SAXSdb — 8si7

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8si7
沉积日期 deposition_date	2023-04-14
结构标题 title	Cryo-EM structure of TRPM7 in GDN detergent in complex with inhibitor VER155008 in closed state
关键词 keywords	;transient receptor potential M family member 7, TRP, channel, TRPM7, TRP channels, membrane protein, magnesium channel, inhibitor, ligand, VER155008 ;; 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	55.45 Å
回转半径 Rg (电子) rg_electron	54.99 Å
零角强度 I(0) i0	3425040000.00
分子量 molecular_weight	549380.0 kDa
排除体积 excluded_volume	710910 Å³
包络体积 envelope_volume	1013600 Å³
水化壳体积 shell_volume	145640 Å³
包络直径 envelope_diameter	177.7 Å
壳层 Rg shell_rg	64.53 Å
包络 Rg envelope_rg	53.60 Å
形状 Rg shape_rg	54.97 Å
总 Rg total_rg	55.32 Å
总原子数 total_atoms	79145
残基数 n_residues	4420
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	176.2 Å
Rg (实空间) rg_real	55.11 Å
Rg 误差 (实空间) rg_real_error	1.30 Å
I(0) (实空间) i0_real	3.4250e+09
I(0) 误差 (实空间) i0_real_error	6.2100e+07
Rg (倒空间) rg_reciprocal	55.73 Å
I(0) (倒空间) i0_reciprocal	3428000000.0000
解质量估计 total_estimate	0.8730
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	75.5 Å
偏度 Skewness skewness	0.087
峰度 Kurtosis kurtosis	-0.433
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	426800000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.845

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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 (7)

Entity 1 polymer

描述 description	Transient receptor potential cation channel subfamily M member 7
分子量 formula_weight	146888.9 kDa
EC 编号 ec_number	2.7.11.1
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	79301

SQKSWIESTLTKRECVYIIPSSKDPHRCLPGCQICQQLVRCFCGRLVKQHACFTASLAMKYSDVKLGEHFNQAIEEWSVEKHTEQSPTDAYGVINFQGGSHSYRAKYVRLSYDTKPEIILQLLLKEWQMELPKLVISVHGGMQKFELHPRIKQLLGKGLIKAAVTTGAWILTGGVNTGVAKHVGDALKEHASRSSRKICTIGIAPWGVIENRNDLVGRDVVAPYQTLLNPLSKLNVLNNLHSHFILVDDGTVGKYGAEVRLRRELEKTINQQRIHARIGQGVPVVALIFEGGPNVILTVLEYLQESPPVPVVVCEGTGRAADLLAYIHKQTEEGGNLPDAAEPDIISTIKKTFNFGQSEAVHLFQTMMECMKKKELITVFHIGSEDHQDIDVAILTALLKGTNASAFDQLILTLAWDRVDIAKNHVFVYGQQWLVGSLEQAMLDALVMDRVSFVKLLIENGVSMHKFLTIPRLEELYNTKQGPTNPMLFHLIRDVKQGNLPPGYKITLIDIGLVIEYLMGGTYRCTYTRKRFRLIYNSLGGNNRRSGRNTSSSTPQLRKSHETFGNRADKKEKMRHNHFIKTAQPYRPKMDASMEEGKKKRTKDEIVDIDDPETKRFPYPLNELLIWACLMKRQVMARFLWQHGEESMAKALVACKIYRSMAYEAKQSDLVDDTSEELKQYSNDFGQLAVELLEQSFRQDETMAMKLLTYELKNWSNSTCLKLAVSSRLRPFVAHTCTQMLLSDMWMGRLNMRKNSWYKVILSILVPPAILMLEYKTKAEMSHIPQSQDAHQMTMEDSENNFHNITEEIPMEVFKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLDSQIGHLQDLSALTVDTLKTLTAQKASEASKVHNEITRELSISKHLAQNLID

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 non-polymer

描述 description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
分子量 formula_weight	760.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	52

Entity 3 non-polymer

描述 description	4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile
分子量 formula_weight	556.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	CHOLESTEROL
分子量 formula_weight	386.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	;2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol ;
分子量 formula_weight	516.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 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	1

Entity 7 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	156

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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	2.59 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	197764

fit	/app/data/saxs_computation/si/8si7/8si7.fit
pddf	/app/data/pr_computation/si/8si7/8si7.pr.out
profile	/app/data/saxs_computation/si/8si7/8si7.dat

Cryo-EM structure of TRPM7 in GDN detergent in complex with inhibitor VER155008 in closed state

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution