SAXSdb — 1nyu

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nyu
沉积日期 deposition_date	2003-02-13
结构标题 title	Crystal Structure of Activin A Bound to the ECD of ActRIIB
关键词 keywords	ACTIVIN, TYPE II, TGF BETA, ACTRIIB, EXTRACELLULAR DOMAIN, MEMBRANE PROTEIN-HORMONE-GROWTH FACTOR COMPLEX; MEMBRANE PROTEIN/HORMONE/GROWTH FACTOR
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	23.11 Å
回转半径 Rg (电子) rg_electron	22.19 Å
零角强度 I(0) i0	22951300.00
分子量 molecular_weight	34089.0 kDa
排除体积 excluded_volume	41542 Å³
包络体积 envelope_volume	56498 Å³
水化壳体积 shell_volume	21794 Å³
包络直径 envelope_diameter	74.2 Å
壳层 Rg shell_rg	28.47 Å
包络 Rg envelope_rg	22.08 Å
形状 Rg shape_rg	22.21 Å
总 Rg total_rg	22.96 Å
总原子数 total_atoms	2375
残基数 n_residues	320
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	74.5 Å
Rg (实空间) rg_real	23.03 Å
Rg 误差 (实空间) rg_real_error	0.44 Å
I(0) (实空间) i0_real	2.2950e+07
I(0) 误差 (实空间) i0_real_error	2.7980e+05
Rg (倒空间) rg_reciprocal	23.05 Å
I(0) (倒空间) i0_reciprocal	22950000.0000
解质量估计 total_estimate	0.9066
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	26.4 Å
偏度 Skewness skewness	0.152
峰度 Kurtosis kurtosis	-0.573
角度范围 angular_range	— – 0.3450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2055000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.996

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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 (2)

Entity 1 polymer

描述 description	activin receptor
分子量 formula_weight	12341.6 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,C
原子数 atom_count	2375

SGRGEAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLPEPLVPR

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 polymer

描述 description	Inhibin beta A chain
分子量 formula_weight	12991.9 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	B,D

GLECDGKVNICCKKQFFVSFKDIGWNDWIIAPSGYHANYCEGECPSHIAGTSGSSLSFHSTVINHYRMRGHSPFANLKSCCVPTKLRPMSMLYYDDGQNIIKKDIQNMIVEECGCS

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	Cricetulus griseus

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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	d1nyua_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.7 — Snake toxin-like
超家族 Superfamily superfamily	g.7.1 — Snake toxin-like
家族 Family family	g.7.1.3 — Extracellular domain of cell surface receptors

结构域编号 domain_id	d1nyub_
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.17.1.2 — Transforming growth factor (TGF)-beta

结构域编号 domain_id	d1nyuc_
类 Class class	g — Small proteins
折叠类型 Fold fold	g.7 — Snake toxin-like
超家族 Superfamily superfamily	g.7.1 — Snake toxin-like
家族 Family family	g.7.1.3 — Extracellular domain of cell surface receptors

结构域编号 domain_id	d1nyud_
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.17.1.2 — Transforming growth factor (TGF)-beta

CATH v4.4 (4 domains)

结构域编号 domain_id	1nyuA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	60 — CD59
同源超家族 H-superfamily homologous superfamily	10 — CD59

结构域编号 domain_id	1nyuB00
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	1nyuC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	60 — CD59
同源超家族 H-superfamily homologous superfamily	10 — CD59

结构域编号 domain_id	1nyuD00
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

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7. 引用文献 (1)

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晶胞边长 a length_a	141.330 Å
晶胞边长 b length_b	141.330 Å
晶胞边长 c length_c	46.021 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	16

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	14.990 Å
R 因子 r_factor	0.2680
R_work r_work	0.2680
R_free r_free	0.2910

fit	/app/data/saxs_computation/ny/1nyu/1nyu.fit
pddf	/app/data/pr_computation/ny/1nyu/1nyu.pr.out
profile	/app/data/saxs_computation/ny/1nyu/1nyu.dat

Crystal Structure of Activin A Bound to the ECD of ActRIIB

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

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)