SAXSdb — 1hl6

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hl6
沉积日期 deposition_date	2003-03-13
结构标题 title	A novel mode of RBD-protein recognition in the Y14-mago complex
关键词 keywords	SIGNAL PROTEIN, RDB, EXON-EXON JUNCTION, OSKAR, RNP, NMD; SIGNAL PROTEIN
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	27.23 Å
回转半径 Rg (电子) rg_electron	26.05 Å
零角强度 I(0) i0	57638000.00
分子量 molecular_weight	59247.0 kDa
排除体积 excluded_volume	74235 Å³
包络体积 envelope_volume	94349 Å³
水化壳体积 shell_volume	30081 Å³
包络直径 envelope_diameter	87.3 Å
壳层 Rg shell_rg	33.53 Å
包络 Rg envelope_rg	25.78 Å
形状 Rg shape_rg	26.05 Å
总 Rg total_rg	26.89 Å
总原子数 total_atoms	4185
残基数 n_residues	510
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	84.3 Å
Rg (实空间) rg_real	27.12 Å
Rg 误差 (实空间) rg_real_error	0.49 Å
I(0) (实空间) i0_real	5.7640e+07
I(0) 误差 (实空间) i0_real_error	8.7530e+05
Rg (倒空间) rg_reciprocal	27.16 Å
I(0) (倒空间) i0_reciprocal	57640000.0000
解质量估计 total_estimate	0.9115
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	34.9 Å
偏度 Skewness skewness	0.180
峰度 Kurtosis kurtosis	-0.501
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8658000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.978

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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	CG8781 PROTEIN
分子量 formula_weight	19042.1 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	4285

MADVLDIDNAEEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR

来源 Source

来源生物 organism	DROSOPHILA MELANOGASTER
通用名 common_name	FRUIT FLY
NCBI 分类编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	MAGO NASHI PROTEIN
分子量 formula_weight	17590.1 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

MSTEDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAFVHQSVMEELKRIIIDSEIMQEDDLPWPPPDRVGRQELEIVIGDEHISFTTSKTGSLVDVNRSKDPEGLRCFYYLVQDLKCLVFSLIGLHFKIKPIPR

来源 Source

来源生物 organism	DROSOPHILA MELANOGASTER
通用名 common_name	FRUIT FLY
NCBI 分类编号 ncbi_taxonomy_id	7227
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	100

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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	d1hl6a_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
家族 Family family	d.58.7.1 — Canonical RBD

结构域编号 domain_id	d1hl6b_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.232 — Mago nashi protein
超家族 Superfamily superfamily	d.232.1 — Mago nashi protein
家族 Family family	d.232.1.1 — Mago nashi protein

结构域编号 domain_id	d1hl6c_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
家族 Family family	d.58.7.1 — Canonical RBD

结构域编号 domain_id	d1hl6d_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.232 — Mago nashi protein
超家族 Superfamily superfamily	d.232.1 — Mago nashi protein
家族 Family family	d.232.1.1 — Mago nashi protein

CATH v4.4 (4 domains)

结构域编号 domain_id	1hl6A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

结构域编号 domain_id	1hl6B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1560 — Mago nashi protein
同源超家族 H-superfamily homologous superfamily	10 — Mago nashi

结构域编号 domain_id	1hl6C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

结构域编号 domain_id	1hl6D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1560 — Mago nashi protein
同源超家族 H-superfamily homologous superfamily	10 — Mago nashi

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7. 引用文献 (1)

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晶胞边长 a length_a	140.177 Å
晶胞边长 b length_b	140.177 Å
晶胞边长 c length_c	68.579 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	I 4
空间群编号 int_tables_number	79
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2720

fit	/app/data/saxs_computation/hl/1hl6/1hl6.fit
pddf	/app/data/pr_computation/hl/1hl6/1hl6.pr.out
profile	/app/data/saxs_computation/hl/1hl6/1hl6.dat

A novel mode of RBD-protein recognition in the Y14-mago complex

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)