SAXSdb — 1fv2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fv2
沉积日期 deposition_date	2000-09-18
结构标题 title	The Hc fragment of tetanus toxin complexed with an analogue of its ganglioside receptor GT1B
关键词 keywords	toxin, carbohydrate, ganglioside, multi-valent binding, receptor; TOXIN
实验方法 method	X-RAY DIFFRACTION

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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	26.58 Å
回转半径 Rg (电子) rg_electron	25.51 Å
零角强度 I(0) i0	46141300.00
分子量 molecular_weight	53405.0 kDa
排除体积 excluded_volume	67123 Å³
包络体积 envelope_volume	83117 Å³
水化壳体积 shell_volume	27640 Å³
包络直径 envelope_diameter	94.0 Å
壳层 Rg shell_rg	32.32 Å
包络 Rg envelope_rg	25.77 Å
形状 Rg shape_rg	25.45 Å
总 Rg total_rg	26.49 Å
总原子数 total_atoms	3767
残基数 n_residues	451
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	85.6 Å
Rg (实空间) rg_real	26.63 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	4.6140e+07
I(0) 误差 (实空间) i0_real_error	6.7890e+05
Rg (倒空间) rg_reciprocal	26.62 Å
I(0) (倒空间) i0_reciprocal	46140000.0000
解质量估计 total_estimate	0.8925
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	28.6 Å
偏度 Skewness skewness	0.395
峰度 Kurtosis kurtosis	-0.411
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8515000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.960

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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 (5)

Entity 1 polymer

描述 description	TETANUS TOXIN HEAVY CHAIN
分子量 formula_weight	53997.8 kDa
EC 编号 ec_number	3.4.24.68
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	3893

MGSSHHHHHHSSGLVPRGSHMKNLDCWVDNEEDIDVILKKSTILNLDINNDIISDISGFNSSVITYPDAQLVPGINGKAIHLVNNESSEVIVHKAMDIEYNDMFNNFTVSFWLRVPKVSASHLEQYGTNEYSIISSMKKHSLSIGSGWSVSLKGNNLIWTLKDSAGEVRQITFRDLPDKFNAYLANKWVFITITNDRLSSANLYINGVLMGSAEITGLGAIREDNNITLKLDRCNNNNQYVSIDKFRIFCKALNPKEIEKLYTSYLSITFLRDFWGNPLRYDTEYYLIPVASSSKDVQLKNITDYMYLTNAPSYTNGKLNIYYRRLYNGLKFIIKRYTPNNEIDSFVKSGDFIKLYVSYNNNEHIVGYPKDGNAFNNLDRILRVGYNAPGIPLYKKMEAVKLRDLKTYSVQLKLYDDKNASLGLVGTHNGQIGNDPNRDILIASNWYFNHLKDKILGCDWYFVPTDEGWTND

来源 Source

来源生物 organism	Clostridium tetani
NCBI 分类编号 ncbi_taxonomy_id	1513
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose ;
分子量 formula_weight	1581.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	ETHYL-TRIMETHYL-SILANE
分子量 formula_weight	102.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	120

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1fv2a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.6 — Clostridium neurotoxins, the second last domain

结构域编号 domain_id	d1fv2a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.4 — STI-like
家族 Family family	b.42.4.2 — Clostridium neurotoxins, C-terminal domain

CATH v4.4 (2 domains)

结构域编号 domain_id	1fv2A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	1fv2A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

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7. 引用文献 (3)

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晶胞边长 a length_a	45.849 Å
晶胞边长 b length_b	52.172 Å
晶胞边长 c length_c	117.353 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.55 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2253
R_work r_work	0.2237
R_free r_free	0.2763

fit	/app/data/saxs_computation/fv/1fv2/1fv2.fit
pddf	/app/data/pr_computation/fv/1fv2/1fv2.pr.out
profile	/app/data/saxs_computation/fv/1fv2/1fv2.dat

The Hc fragment of tetanus toxin complexed with an analogue of its ganglioside receptor GT1B

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

精修参数 Refinement

衍射实验 Diffraction