2e7s

Crystal structure of the yeast Sec2p GEF domain

Method: X-RAY DIFFRACTION D_max: 219.8 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2e7s
沉积日期 deposition_date	2007-01-12
结构标题 title	Crystal structure of the yeast Sec2p GEF domain
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	80.61 Å
回转半径 Rg (电子) rg_electron	82.04 Å
零角强度 I(0) i0	1157820000.00
分子量 molecular_weight	272550.0 kDa
排除体积 excluded_volume	336470 Å³
包络体积 envelope_volume	891640 Å³
水化壳体积 shell_volume	102820 Å³
包络直径 envelope_diameter	322.2 Å
壳层 Rg shell_rg	67.06 Å
包络 Rg envelope_rg	77.32 Å
形状 Rg shape_rg	82.07 Å
总 Rg total_rg	81.56 Å
总原子数 total_atoms	19008
残基数 n_residues	2279
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	219.8 Å
Rg (实空间) rg_real	77.71 Å
Rg 误差 (实空间) rg_real_error	1.03 Å
I(0) (实空间) i0_real	1.1330e+09
I(0) 误差 (实空间) i0_real_error	2.2440e+07
Rg (倒空间) rg_reciprocal	79.34 Å
I(0) (倒空间) i0_reciprocal	1154000000.0000
解质量估计 total_estimate	0.8622
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	92.5 Å
偏度 Skewness skewness	0.292
峰度 Kurtosis kurtosis	-0.400
角度范围 angular_range	— – 0.0950 Å⁻¹
当前正则化参数 α current_alpha	0.0624
最高正则化参数 α highest_alpha	165700000.0000
实空间数据点数 n_real_points	20
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 0.985; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.073

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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)

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

结构域编号 domain_id	d2e7sa1
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	d2e7sb_
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	d2e7sc_
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	d2e7sd_
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	d2e7se_
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	d2e7sf_
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	d2e7sg_
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	d2e7sh_
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	d2e7si_
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	d2e7sj_
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	d2e7sk_
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	d2e7sl_
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	d2e7sm_
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	d2e7sn_
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	d2e7so_
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	d2e7sp_
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	d2e7sq_
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	d2e7sr_
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	d2e7ss_
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	d2e7st_
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

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7. 引用文献 (1)

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晶胞边长 a length_a	101.937 Å
晶胞边长 b length_b	176.569 Å
晶胞边长 c length_c	181.453 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	40

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2290
R_free r_free	0.2850

描述 description	Rab guanine nucleotide exchange factor SEC2
分子量 formula_weight	15780.5 kDa
突变 mutation	M115L/K121M/T142M
来源方法 src_method	man
拷贝数 entity_count	20

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
原子数 atom_count	19270

Crystal structure of the yeast Sec2p GEF domain

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 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	262

fit	/app/data/saxs_computation/e7/2e7s/2e7s.fit
pddf	/app/data/pr_computation/e7/2e7s/2e7s.pr.out
profile	/app/data/saxs_computation/e7/2e7s/2e7s.dat