8thj

;Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Haemophilus influenzae (antiparallel dimer) ;

Method: ELECTRON MICROSCOPY D_max: 127.3 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	8thj
沉积日期 deposition_date	2023-07-16
结构标题 title	;Cryo-EM structure of the Tripartite ATP-independent Periplasmic (TRAP) transporter SiaQM from Haemophilus influenzae (antiparallel dimer) ;
关键词 keywords	Sugar transport, sialic acid, TRAP transporter, secondary active transport, ion transporter superfamily, TRANSPORT PROTEIN; TRANSPORT 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	39.18 Å
回转半径 Rg (电子) rg_electron	38.68 Å
零角强度 I(0) i0	211738000.00
分子量 molecular_weight	136960.0 kDa
排除体积 excluded_volume	179220 Å³
包络体积 envelope_volume	230090 Å³
水化壳体积 shell_volume	50552 Å³
包络直径 envelope_diameter	128.0 Å
壳层 Rg shell_rg	43.99 Å
包络 Rg envelope_rg	38.05 Å
形状 Rg shape_rg	38.65 Å
总 Rg total_rg	39.16 Å
总原子数 total_atoms	9642
残基数 n_residues	1230
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	127.3 Å
Rg (实空间) rg_real	39.25 Å
Rg 误差 (实空间) rg_real_error	1.20 Å
I(0) (实空间) i0_real	2.1170e+08
I(0) 误差 (实空间) i0_real_error	4.0480e+06
Rg (倒空间) rg_reciprocal	39.22 Å
I(0) (倒空间) i0_reciprocal	211700000.0000
解质量估计 total_estimate	0.8911
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	38.2 Å
偏度 Skewness skewness	0.309
峰度 Kurtosis kurtosis	-0.617
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	29480000.0000
实空间数据点数 n_real_points	41
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: 0.981; Smooth: 0.878

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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	Sialic acid TRAP transporter permease protein SiaT
分子量 formula_weight	72046.8 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	9642

MGGSHHHHHHGMASMTGGQQMGRDLYDDDDKDRWGSELEMKYINKLEEWLGGALFIAIFGILIAQILSRQVFHSPLIWSEELAKLLFVYVGMLGISVAVRKQEHVFIDFLTNLMPEKIRKFTNTFVQLLVFICIFLFIHFGIRTFNGASFPIDALGGISEKWIFAALPVVAILMMFRFIQAQTLNFKTGKSYLPATFFIISAVILFAILFFAPDWFKVLRISNYIKLGSSSVYVALLVWLIIMFIGVPVGWSLFIATLLYFSMTRWNVVNAATEKLVYSLDSFPLLAVPFYILTGILMNTGGITERIFNFAKALLGHYTGGMGHVNIGASLLFSGMSGSALADAGGLGQLEIKAMRDAGYDDDICGGITAASCIIGPLVPPSIAMIIYGVIANESIAKLFIAGFIPGVLITLALMAMNYRIAKKRGYPRTPKATREQLCSSFKQSFWAILTPLLIIGGIFSGLFSPTESAIVAAAYSVIIGKFVYKELTLKSLFNSCIEAMAITGVVALMIMTVTFFGDMIAREQVAMRVADVFVAVADSPLTVLIMINALLLFLGMFIDALALQFLVLPMLIPIAMQFNIDLIFFGVMTTLNMMVGILTPPMGMALFVVARVGNMSVSTVTKGVLPFLIPVFVTLVLITIFPQIITFVPNLLIP

来源 Source

来源生物 organism	Haemophilus influenzae Rd KW20
NCBI 分类编号 ncbi_taxonomy_id	71421
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	PHOSPHATIDYLETHANOLAMINE
分子量 formula_weight	734.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
分子量 formula_weight	751.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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7. 引用文献 (2)

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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	2.99 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	225044

fit	/app/data/saxs_computation/th/8thj/8thj.fit
pddf	/app/data/pr_computation/th/8thj/8thj.pr.out
profile	/app/data/saxs_computation/th/8thj/8thj.dat