1jth

;Crystal structure and biophysical properties of a complex between the N-terminal region of SNAP25 and the SNARE region of syntaxin 1a ;

Method: X-RAY DIFFRACTION D_max: 104.1 Å Quality: REASONABLE

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	1jth
沉积日期 deposition_date	2001-08-21
结构标题 title	;Crystal structure and biophysical properties of a complex between the N-terminal region of SNAP25 and the SNARE region of syntaxin 1a ;
关键词 keywords	coiled-coil, polar layer, 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	27.08 Å
回转半径 Rg (电子) rg_electron	27.68 Å
零角强度 I(0) i0	16277800.00
分子量 molecular_weight	28820.0 kDa
排除体积 excluded_volume	35258 Å³
包络体积 envelope_volume	45263 Å³
水化壳体积 shell_volume	16408 Å³
包络直径 envelope_diameter	109.2 Å
壳层 Rg shell_rg	29.50 Å
包络 Rg envelope_rg	28.89 Å
形状 Rg shape_rg	27.71 Å
总 Rg total_rg	27.77 Å
总原子数 total_atoms	2005
残基数 n_residues	249
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	104.1 Å
Rg (实空间) rg_real	27.78 Å
Rg 误差 (实空间) rg_real_error	1.55 Å
I(0) (实空间) i0_real	1.6280e+07
I(0) 误差 (实空间) i0_real_error	2.8780e+05
Rg (倒空间) rg_reciprocal	27.56 Å
I(0) (倒空间) i0_reciprocal	16280000.0000
解质量估计 total_estimate	0.6554
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	19.4 Å
偏度 Skewness skewness	0.737
峰度 Kurtosis kurtosis	-0.144
角度范围 angular_range	— – 0.2950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6524000.0000
实空间数据点数 n_real_points	60
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.169; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.017; Smooth: 0.992

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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	SNAP25
分子量 formula_weight	9525.6 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	A,C
原子数 atom_count	2057

MAEDADMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLERIEEGMDQINKDMKEAEKNLTDLG

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21

Entity 2 polymer

描述 description	syntaxin 1a
分子量 formula_weight	9102.5 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

ALSEIETRHSEIIKLENSIRELHDMFMDMAMLVESQGEMIDRIEYNVEHAVDYVERAVSDTKKAVKYQSKARRKKIM

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI 分类编号 ncbi_taxonomy_id	10116
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	52

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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	d1jtha_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.15 — SNARE fusion complex
家族 Family family	h.1.15.1 — SNARE fusion complex

结构域编号 domain_id	d1jthb_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.15 — SNARE fusion complex
家族 Family family	h.1.15.1 — SNARE fusion complex

结构域编号 domain_id	d1jthc_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.15 — SNARE fusion complex
家族 Family family	h.1.15.1 — SNARE fusion complex

结构域编号 domain_id	d1jthd_
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.15 — SNARE fusion complex
家族 Family family	h.1.15.1 — SNARE fusion complex

CATH v4.4 (4 domains)

结构域编号 domain_id	1jthA00
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	110 —

结构域编号 domain_id	1jthB00
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	110 —

结构域编号 domain_id	1jthC00
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	110 —

结构域编号 domain_id	1jthD00
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	110 —

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7. 引用文献 (1)

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晶胞边长 a length_a	59.400 Å
晶胞边长 b length_b	65.780 Å
晶胞边长 c length_c	80.100 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	99.50 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2660
R_free r_free	0.2890

fit	/app/data/saxs_computation/jt/1jth/1jth.fit
pddf	/app/data/pr_computation/jt/1jth/1jth.pr.out
profile	/app/data/saxs_computation/jt/1jth/1jth.dat

;Crystal structure and biophysical properties of a complex between the N-terminal region of SNAP25 and the SNARE region of syntaxin 1a ;

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)