SAXSdb — 1fsj

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fsj
沉积日期 deposition_date	2000-09-11
结构标题 title	CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN
关键词 keywords	zinc containing enzyme, HNH-motif, HYDROLASE; HYDROLASE
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	26.87 Å
回转半径 Rg (电子) rg_electron	26.32 Å
零角强度 I(0) i0	66338800.00
分子量 molecular_weight	60244.0 kDa
排除体积 excluded_volume	74253 Å³
包络体积 envelope_volume	95567 Å³
水化壳体积 shell_volume	30475 Å³
包络直径 envelope_diameter	80.8 Å
壳层 Rg shell_rg	33.56 Å
包络 Rg envelope_rg	25.96 Å
形状 Rg shape_rg	26.31 Å
总 Rg total_rg	27.14 Å
总原子数 total_atoms	4229
残基数 n_residues	530
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	75.8 Å
Rg (实空间) rg_real	26.68 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	6.6340e+07
I(0) 误差 (实空间) i0_real_error	8.6340e+05
Rg (倒空间) rg_reciprocal	26.74 Å
I(0) (倒空间) i0_reciprocal	66340000.0000
解质量估计 total_estimate	0.9140
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	38.5 Å
偏度 Skewness skewness	0.015
峰度 Kurtosis kurtosis	-0.689
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	18220000.0000
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: 0.988; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.919

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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	COLICIN E9
分子量 formula_weight	15120.0 kDa
EC 编号 ec_number	3.1.21.1
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,C,D,E
原子数 atom_count	4546

MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 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	4

Entity 3 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 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	317

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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	d1fsjb_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.4 — His-Me finger endonucleases
超家族 Superfamily superfamily	d.4.1 — His-Me finger endonucleases
家族 Family family	d.4.1.1 — HNH-motif

结构域编号 domain_id	d1fsjc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.4 — His-Me finger endonucleases
超家族 Superfamily superfamily	d.4.1 — His-Me finger endonucleases
家族 Family family	d.4.1.1 — HNH-motif

结构域编号 domain_id	d1fsjd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.4 — His-Me finger endonucleases
超家族 Superfamily superfamily	d.4.1 — His-Me finger endonucleases
家族 Family family	d.4.1.1 — HNH-motif

结构域编号 domain_id	d1fsje_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.4 — His-Me finger endonucleases
超家族 Superfamily superfamily	d.4.1 — His-Me finger endonucleases
家族 Family family	d.4.1.1 — HNH-motif

CATH v4.4 (4 domains)

结构域编号 domain_id	1fsjB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
同源超家族 H-superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

结构域编号 domain_id	1fsjC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
同源超家族 H-superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

结构域编号 domain_id	1fsjD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
同源超家族 H-superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

结构域编号 domain_id	1fsjE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
同源超家族 H-superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

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7. 引用文献 (2)

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晶胞边长 a length_a	57.120 Å
晶胞边长 b length_b	82.960 Å
晶胞边长 c length_c	113.660 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	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	—
R_work r_work	0.1890
R_free r_free	0.2220

fit	/app/data/saxs_computation/fs/1fsj/1fsj.fit
pddf	/app/data/pr_computation/fs/1fsj/1fsj.pr.out
profile	/app/data/saxs_computation/fs/1fsj/1fsj.dat

CRYSTAL STRUCTURE OF THE E9 DNASE 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 (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 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)