SAXSdb — 2fju

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2fju
沉积日期 deposition_date	2006-01-03
结构标题 title	Activated Rac1 bound to its effector phospholipase C beta 2
关键词 keywords	Protein-protein complex, SIGNALING PROTEIN, APOPTOSIS-HYDROLASE COMPLEX; SIGNALING PROTEIN,APOPTOSIS/HYDROLASE
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	33.71 Å
回转半径 Rg (电子) rg_electron	33.28 Å
零角强度 I(0) i0	150464000.00
分子量 molecular_weight	100080.0 kDa
排除体积 excluded_volume	126020 Å³
包络体积 envelope_volume	157520 Å³
水化壳体积 shell_volume	40013 Å³
包络直径 envelope_diameter	113.3 Å
壳层 Rg shell_rg	39.29 Å
包络 Rg envelope_rg	33.46 Å
形状 Rg shape_rg	33.26 Å
总 Rg total_rg	33.81 Å
总原子数 total_atoms	7028
残基数 n_residues	873
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	108.8 Å
Rg (实空间) rg_real	33.75 Å
Rg 误差 (实空间) rg_real_error	0.96 Å
I(0) (实空间) i0_real	1.5050e+08
I(0) 误差 (实空间) i0_real_error	2.5810e+06
Rg (倒空间) rg_reciprocal	33.73 Å
I(0) (倒空间) i0_reciprocal	150500000.0000
解质量估计 total_estimate	0.8878
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.4 Å
偏度 Skewness skewness	0.319
峰度 Kurtosis kurtosis	-0.574
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	35290000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.836

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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 (6)

Entity 1 polymer

描述 description	Ras-related C3 botulinum toxin substrate 1
分子量 formula_weight	19797.8 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	A
原子数 atom_count	7514

MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLS

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	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 2
分子量 formula_weight	91033.9 kDa
EC 编号 ec_number	3.1.4.11
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	B

MSLLNPVLLPPKVKAYLSQGERFIKWDDETTVASPVILRVDPKGYYLYWTYQSKEMEFLDITSIRDTRFGKFAKMPKSQKLRDVFNMDFPDNSFLLKTLTVVSGPDMVDLTFHNFVSYKENVGKAWAEDVLALVKHPLTANASRSTFLDKILVKLKMQLNSEGKIPVKNFFQMFPADRKRVEAALSACHLPKGKNDAINPEDFPEPVYKSFLMSLCPRPEIDEIFTSYHAKAKPYMTKEHLTKFINQKQRDSRLNSLLFPPARPDQVQGLIDKYEPSGINAQRGQLSPEGMVWFLCGPENSVLAQDKLLLHHDMTQPLNHYFINSSHNTYLTAGQFSGLSSAEMYRQVLLSGCRCVELDCWKGKPPDEEPIITHGFTMTTDIFFKEAIEAIAESAFKTSPYPIILSFENHVDSPRQQAKMAEYCRTIFGDMLLTEPLEKFPLKPGVPLPSPEDLRGKILIKNKKNQFSGPTSSSKDTGGEAEGSSPPSAPAVWAGEEGTELEEEEVEEEEEEESGNLDEEEIKKMQSDEGTAGLEVTAYEEMSSLVNYIQPTKFVSFEFSAQKNRSYVISSFTELKAYDLLSKASVQFVDYNKRQMSRIYPKGTRMDSSNYMPQMFWNAGCQMVALNFQTMDLPMQQNMAVFEFNGQSGYLLKHEFMRRPDKQFNPFSVDRIDVVVATTLSITVISGQFLSERSVRTYVEVELFGLPGDPKRRYRTKLSPSTNSINPVWKEEPFVFEKILMPELASLRVAVMEEGNKFLGHRIIPINALNSGYHHLCLHSESNMPLTMPALFIFLEMKD

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	Spodoptera frugiperda

Entity 3 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 4 non-polymer

描述 description	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
分子量 formula_weight	539.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 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	486

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2fjua_
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	d2fjub1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.39 — EF Hand-like
超家族 Superfamily superfamily	a.39.1 — EF-hand
家族 Family family	a.39.1.7 — EF-hand modules in multidomain proteins

结构域编号 domain_id	d2fjub2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.7 — C2 domain-like
超家族 Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
家族 Family family	b.7.1.1 — PLC-like (P variant)

结构域编号 domain_id	d2fjub3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.55 — PH domain-like barrel
超家族 Superfamily superfamily	b.55.1 — PH domain-like
家族 Family family	b.55.1.1 — Pleckstrin-homology domain (PH domain)

结构域编号 domain_id	d2fjub4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.18 — PLC-like phosphodiesterases
家族 Family family	c.1.18.1 — Mammalian PLC

CATH v4.4 (5 domains)

结构域编号 domain_id	2fjuA00
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	2fjuB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	29 — PH-domain like
同源超家族 H-superfamily homologous superfamily	240 —

结构域编号 domain_id	2fjuB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	238 — Recoverin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — EF-hand

结构域编号 domain_id	2fjuB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	190 — Phosphatidylinositol (PI) phosphodiesterase

结构域编号 domain_id	2fjuB04
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	150 — C2 domain

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7. 引用文献 (1)

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晶胞边长 a length_a	185.822 Å
晶胞边长 b length_b	185.822 Å
晶胞边长 c length_c	93.823 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	—
R_work r_work	0.2084
R_free r_free	0.2261

fit	/app/data/saxs_computation/fj/2fju/2fju.fit
pddf	/app/data/pr_computation/fj/2fju/2fju.pr.out
profile	/app/data/saxs_computation/fj/2fju/2fju.dat

Activated Rac1 bound to its effector phospholipase C beta 2

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)