SAXSdb — 2eqb

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2eqb
沉积日期 deposition_date	2007-03-30
结构标题 title	Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate complex
关键词 keywords	coiled coil, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
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	34.36 Å
回转半径 Rg (电子) rg_electron	34.86 Å
零角强度 I(0) i0	29963300.00
分子量 molecular_weight	41427.0 kDa
排除体积 excluded_volume	51392 Å³
包络体积 envelope_volume	68869 Å³
水化壳体积 shell_volume	20897 Å³
包络直径 envelope_diameter	140.2 Å
壳层 Rg shell_rg	31.74 Å
包络 Rg envelope_rg	36.55 Å
形状 Rg shape_rg	34.87 Å
总 Rg total_rg	34.57 Å
总原子数 total_atoms	2909
残基数 n_residues	357
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	134.8 Å
Rg (实空间) rg_real	35.16 Å
Rg 误差 (实空间) rg_real_error	2.03 Å
I(0) (实空间) i0_real	2.9960e+07
I(0) 误差 (实空间) i0_real_error	5.5850e+05
Rg (倒空间) rg_reciprocal	34.66 Å
I(0) (倒空间) i0_reciprocal	29950000.0000
解质量估计 total_estimate	0.6790
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	26.4 Å
偏度 Skewness skewness	0.778
峰度 Kurtosis kurtosis	0.060
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1881000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.281; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.105; Smooth: 0.875

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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 (4)

Entity 1 polymer

描述 description	Ras-related protein SEC4
分子量 formula_weight	19447.2 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	A
原子数 atom_count	3023

GPLGSSIMKILLIGDSGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDSN

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Rab guanine nucleotide exchange factor SEC2
分子量 formula_weight	11391.6 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	B,C

GPLGSNYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREKDT

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 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	2

Entity 4 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	114

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6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d2eqba2
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	d2eqba3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2eqbb1
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.33 — Sec2 N-terminal region
家族 Family family	h.1.33.1 — Sec2 N-terminal region

结构域编号 domain_id	d2eqbb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2eqbc2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.33 — Sec2 N-terminal region
家族 Family family	h.1.33.1 — Sec2 N-terminal region

结构域编号 domain_id	d2eqbc3
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

结构域编号 domain_id	2eqbA00
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	2eqbB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	4880 —

结构域编号 domain_id	2eqbC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	4880 —

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7. 引用文献 (1)

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晶胞边长 a length_a	116.581 Å
晶胞边长 b length_b	117.422 Å
晶胞边长 c length_c	123.332 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 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	48.080 Å
R 因子 r_factor	0.2730
R_work r_work	0.2730
R_free r_free	0.2980

fit	/app/data/saxs_computation/eq/2eqb/2eqb.fit
pddf	/app/data/pr_computation/eq/2eqb/2eqb.pr.out
profile	/app/data/saxs_computation/eq/2eqb/2eqb.dat

Crystal structure of the Rab GTPase Sec4p, the Sec2p GEF domain, and phosphate 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

5. 实体与聚合体信息 (4)

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 water

6. 折叠分类 (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)