SAXSdb — 1joc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1joc
沉积日期 deposition_date	2001-07-27
结构标题 title	EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-diphosphate
关键词 keywords	FYVE domain, inositol 3-phosphate binding, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	32.12 Å
回转半径 Rg (电子) rg_electron	33.69 Å
零角强度 I(0) i0	17293900.00
分子量 molecular_weight	28624.0 kDa
排除体积 excluded_volume	34430 Å³
包络体积 envelope_volume	49575 Å³
水化壳体积 shell_volume	15286 Å³
包络直径 envelope_diameter	117.2 Å
壳层 Rg shell_rg	32.16 Å
包络 Rg envelope_rg	34.55 Å
形状 Rg shape_rg	33.69 Å
总 Rg total_rg	33.55 Å
总原子数 total_atoms	1969
残基数 n_residues	246
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	115.7 Å
Rg (实空间) rg_real	33.30 Å
Rg 误差 (实空间) rg_real_error	1.71 Å
I(0) (实空间) i0_real	1.7290e+07
I(0) 误差 (实空间) i0_real_error	3.1350e+05
Rg (倒空间) rg_reciprocal	32.80 Å
I(0) (倒空间) i0_reciprocal	17290000.0000
解质量估计 total_estimate	0.6194
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	18.9 Å
偏度 Skewness skewness	0.750
峰度 Kurtosis kurtosis	-0.390
角度范围 angular_range	— – 0.2450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	527400.0000
实空间数据点数 n_real_points	50
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.220; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.032; Smooth: 0.357

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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	Early Endosomal Autoantigen 1
分子量 formula_weight	14139.1 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,B
原子数 atom_count	2025

NNQDERRALLERCLKGEGEIEKLQTKVLELQRKLDNTTAAVQELGRENQSLQIKHTQALNRKWAEDNEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKNALTPSSKKPVRVCDACFNDLQG

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 BL21(DE3)

Entity 2 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER
分子量 formula_weight	340.1 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	56

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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	d1joca1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.50 — FYVE/PHD zinc finger
超家族 Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
家族 Family family	g.50.1.1 — FYVE, a phosphatidylinositol-3-phosphate binding domain

结构域编号 domain_id	d1joca2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.21 — Eea1 homodimerisation domain
家族 Family family	h.1.21.1 — Eea1 homodimerisation domain

结构域编号 domain_id	d1jocb1
类 Class class	g — Small proteins
折叠类型 Fold fold	g.50 — FYVE/PHD zinc finger
超家族 Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
家族 Family family	g.50.1.1 — FYVE, a phosphatidylinositol-3-phosphate binding domain

结构域编号 domain_id	d1jocb2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.21 — Eea1 homodimerisation domain
家族 Family family	h.1.21.1 — Eea1 homodimerisation domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1jocA01
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	390 — L1 transposable element, trimerization domain

结构域编号 domain_id	1jocA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	40 — Herpes Virus-1
同源超家族 H-superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

结构域编号 domain_id	1jocB01
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	390 — L1 transposable element, trimerization domain

结构域编号 domain_id	1jocB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	40 — Herpes Virus-1
同源超家族 H-superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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7. 引用文献 (1)

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晶胞边长 a length_a	36.528 Å
晶胞边长 b length_b	85.096 Å
晶胞边长 c length_c	88.036 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2210
R_free r_free	0.2810

fit	/app/data/saxs_computation/jo/1joc/1joc.fit
pddf	/app/data/pr_computation/jo/1joc/1joc.pr.out
profile	/app/data/saxs_computation/jo/1joc/1joc.dat

EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-diphosphate

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 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)