SAXSdb — 1fvf

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fvf
沉积日期 deposition_date	2000-09-19
结构标题 title	CRYSTAL STRUCTURE ANALYSIS OF NEURONAL SEC1 FROM THE SQUID L. PEALEI
关键词 keywords	PARALLEL BETA-SHEETS, LEFT-HAND TURN CONNECTION, HELICAL BUNDLE, DIMER, 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	39.60 Å
回转半径 Rg (电子) rg_electron	39.03 Å
零角强度 I(0) i0	234743000.00
分子量 molecular_weight	125110.0 kDa
排除体积 excluded_volume	156820 Å³
包络体积 envelope_volume	209890 Å³
水化壳体积 shell_volume	45549 Å³
包络直径 envelope_diameter	130.9 Å
壳层 Rg shell_rg	44.39 Å
包络 Rg envelope_rg	38.05 Å
形状 Rg shape_rg	39.07 Å
总 Rg total_rg	39.21 Å
总原子数 total_atoms	8786
残基数 n_residues	1086
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	126.6 Å
Rg (实空间) rg_real	39.67 Å
Rg 误差 (实空间) rg_real_error	1.24 Å
I(0) (实空间) i0_real	2.3470e+08
I(0) 误差 (实空间) i0_real_error	3.8760e+06
Rg (倒空间) rg_reciprocal	39.64 Å
I(0) (倒空间) i0_reciprocal	234700000.0000
解质量估计 total_estimate	0.8927
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	38.0 Å
偏度 Skewness skewness	0.235
峰度 Kurtosis kurtosis	-0.815
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	34850000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.928

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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 (1)

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1fvfa_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.25 — Sec1/munc18-like (SM) proteins
超家族 Superfamily superfamily	e.25.1 — Sec1/munc18-like (SM) proteins
家族 Family family	e.25.1.1 — Sec1/munc18-like (SM) proteins

结构域编号 domain_id	d1fvfb_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.25 — Sec1/munc18-like (SM) proteins
超家族 Superfamily superfamily	e.25.1 — Sec1/munc18-like (SM) proteins
家族 Family family	e.25.1.1 — Sec1/munc18-like (SM) proteins

CATH v4.4 (8 domains)

结构域编号 domain_id	1fvfA01
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	1910 — Sec1/Munc18 (SM) protein, domain 2

结构域编号 domain_id	1fvfA02
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	2060 — Sec1/Munc18 (SM) protein, domain 1

结构域编号 domain_id	1fvfA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	830 — Syntaxin Binding Protein 1; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Sec1/Munc18 (SM) protein, domain 3a

结构域编号 domain_id	1fvfA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	60 —

结构域编号 domain_id	1fvfB01
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	1910 — Sec1/Munc18 (SM) protein, domain 2

结构域编号 domain_id	1fvfB02
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	2060 — Sec1/Munc18 (SM) protein, domain 1

结构域编号 domain_id	1fvfB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	830 — Syntaxin Binding Protein 1; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Sec1/Munc18 (SM) protein, domain 3a

结构域编号 domain_id	1fvfB04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	25 — Alpha Horseshoe
拓扑 Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
同源超家族 H-superfamily homologous superfamily	60 —

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7. 引用文献 (3)

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晶胞边长 a length_a	118.517 Å
晶胞边长 b length_b	118.517 Å
晶胞边长 c length_c	192.621 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	12

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	12.000 Å
R 因子 r_factor	0.2449
R_work r_work	0.2426
R_free r_free	0.2876

描述 description	SEC1
分子量 formula_weight	67830.7 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	8786

CRYSTAL STRUCTURE ANALYSIS OF NEURONAL SEC1 FROM THE SQUID L. PEALEI

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 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

CATH v4.4 (8 domains)

7. 引用文献 (3)

8. 文件与曲线 (10)

Files (7)

Curves (3)

来源生物 organism	Loligo pealei
NCBI 分类编号 ncbi_taxonomy_id	6621
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/fv/1fvf/1fvf.fit
pddf	/app/data/pr_computation/fv/1fvf/1fvf.pr.out
profile	/app/data/saxs_computation/fv/1fvf/1fvf.dat