SAXSdb — 1www

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1www
沉积日期 deposition_date	1999-03-12
结构标题 title	NGF IN COMPLEX WITH DOMAIN 5 OF THE TRKA RECEPTOR
关键词 keywords	COMPLEX, TRKA RECEPTOR, NERVE GROWTH FACTOR, CYSTEINE KNOT, IMMUNOGLOBULIN LIKE DOMAIN, NERVE GROWTH FACTOR-TRKA COMPLEX COMPLEX; NERVE GROWTH FACTOR/TRKA COMPLEX
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	26.00 Å
回转半径 Rg (电子) rg_electron	25.68 Å
零角强度 I(0) i0	37908900.00
分子量 molecular_weight	46690.0 kDa
排除体积 excluded_volume	58013 Å³
包络体积 envelope_volume	72124 Å³
水化壳体积 shell_volume	24906 Å³
包络直径 envelope_diameter	98.4 Å
壳层 Rg shell_rg	31.00 Å
包络 Rg envelope_rg	25.98 Å
形状 Rg shape_rg	25.71 Å
总 Rg total_rg	26.20 Å
总原子数 total_atoms	3283
残基数 n_residues	419
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	94.6 Å
Rg (实空间) rg_real	26.12 Å
Rg 误差 (实空间) rg_real_error	0.95 Å
I(0) (实空间) i0_real	3.7910e+07
I(0) 误差 (实空间) i0_real_error	6.0940e+05
Rg (倒空间) rg_reciprocal	26.08 Å
I(0) (倒空间) i0_reciprocal	37910000.0000
解质量估计 total_estimate	0.8379
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	26.4 Å
偏度 Skewness skewness	0.505
峰度 Kurtosis kurtosis	-0.063
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9141000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.702; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.815; Smooth: 0.969

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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	PROTEIN (NERVE GROWTH FACTOR)
分子量 formula_weight	13515.4 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	V,W
原子数 atom_count	3545

SSSHPIFHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKAVRRA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	PROTEIN (TRKA RECEPTOR)
分子量 formula_weight	11107.5 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	X,Y

VSFPASVQLHTAVEMHHWCIPFSVDGQPAPSLRWLFNGSVLNETSFIFTEFLEPAANETVRHGCLRLNQPTHVNNGNYTLLAANPFGQASASIMAAFMDNP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 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	262

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1wwwv_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.17 — Cystine-knot cytokines
超家族 Superfamily superfamily	g.17.1 — Cystine-knot cytokines
家族 Family family	g.17.1.3 — Neurotrophin

结构域编号 domain_id	d1wwww_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.17 — Cystine-knot cytokines
超家族 Superfamily superfamily	g.17.1 — Cystine-knot cytokines
家族 Family family	g.17.1.3 — Neurotrophin

结构域编号 domain_id	d1wwwx_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.4 — I set domains

结构域编号 domain_id	d1wwwy_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.4 — I set domains

CATH v4.4 (4 domains)

结构域编号 domain_id	1wwwV00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	90 — Cystine Knot Cytokines, subunit B
同源超家族 H-superfamily homologous superfamily	10 — Cystine-knot cytokines

结构域编号 domain_id	1wwwW00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	90 — Cystine Knot Cytokines, subunit B
同源超家族 H-superfamily homologous superfamily	10 — Cystine-knot cytokines

结构域编号 domain_id	1wwwX00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1wwwY00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (1)

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晶胞边长 a length_a	58.245 Å
晶胞边长 b length_b	53.735 Å
晶胞边长 c length_c	77.101 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.34 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

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	2.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.1890
R_free r_free	0.2660

fit	/app/data/saxs_computation/ww/1www/1www.fit
pddf	/app/data/pr_computation/ww/1www/1www.pr.out
profile	/app/data/saxs_computation/ww/1www/1www.dat

NGF IN COMPLEX WITH DOMAIN 5 OF THE TRKA RECEPTOR

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

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)