SAXSdb — 1nvv

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nvv
沉积日期 deposition_date	2003-02-04
结构标题 title	Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS
关键词 keywords	Proto-oncogene, GTP-binding, Guanine-nucleotide releasing factor, SIGNALING PROTEIN; SIGNALING 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	31.58 Å
回转半径 Rg (电子) rg_electron	30.73 Å
零角强度 I(0) i0	143126000.00
分子量 molecular_weight	93805.0 kDa
排除体积 excluded_volume	116950 Å³
包络体积 envelope_volume	147810 Å³
水化壳体积 shell_volume	40107 Å³
包络直径 envelope_diameter	120.6 Å
壳层 Rg shell_rg	37.74 Å
包络 Rg envelope_rg	30.95 Å
形状 Rg shape_rg	30.72 Å
总 Rg total_rg	31.34 Å
总原子数 total_atoms	6593
残基数 n_residues	801
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	113.7 Å
Rg (实空间) rg_real	31.60 Å
Rg 误差 (实空间) rg_real_error	1.01 Å
I(0) (实空间) i0_real	1.4310e+08
I(0) 误差 (实空间) i0_real_error	2.1770e+06
Rg (倒空间) rg_reciprocal	31.59 Å
I(0) (倒空间) i0_reciprocal	143100000.0000
解质量估计 total_estimate	0.8549
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	36.4 Å
偏度 Skewness skewness	0.386
峰度 Kurtosis kurtosis	-0.209
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	44340000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.949

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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 (7)

Entity 1 polymer

描述 description	Transforming protein p21/H-RAS-1
分子量 formula_weight	18783.1 kDa
突变 mutation	Y64A
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	Q
原子数 atom_count	6908

MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEASAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

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 BL21(DE3)

Entity 2 polymer

描述 description	Transforming protein p21/H-RAS-1
分子量 formula_weight	18875.2 kDa
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	R

MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

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 BL21(DE3)

Entity 3 polymer

描述 description	Son of sevenless protein homolog 1
分子量 formula_weight	56532.7 kDa
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	S

QMRLPSADVYRFAEPDSEENIIFEENMQPKAGIPIIKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIARDNGPGHNITFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNPR

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 BL21(DE3)

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	5

Entity 6 non-polymer

描述 description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
分子量 formula_weight	522.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	315

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1nvvq_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1nvvr_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
超家族 Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
家族 Family family	c.37.1.8 — G proteins

结构域编号 domain_id	d1nvvs_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.117 — Ras GEF
超家族 Superfamily superfamily	a.117.1 — Ras GEF
家族 Family family	a.117.1.1 — Ras GEF

CATH v4.4 (4 domains)

结构域编号 domain_id	1nvvQ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1nvvR00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

结构域编号 domain_id	1nvvS01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	870 — Son of sevenless (SoS) protein; Chain S, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Son of sevenless (SoS) protein Chain: S domain 1

结构域编号 domain_id	1nvvS02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	840 — Son of Sevenless (SoS) protein; Chain S, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Ras guanine-nucleotide exchange factors catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	184.163 Å
晶胞边长 b length_b	184.163 Å
晶胞边长 c length_c	179.076 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 2 2
空间群编号 int_tables_number	97
晶系 crystal_system	—

分辨率 resolution	2.180 Å
最低分辨率 resolution_low	64.190 Å
R 因子 r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2410

fit	/app/data/saxs_computation/nv/1nvv/1nvv.fit
pddf	/app/data/pr_computation/nv/1nvv/1nvv.pr.out
profile	/app/data/saxs_computation/nv/1nvv/1nvv.dat

Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS

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 (7)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)