1p3i

;Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants ;

Method: X-RAY DIFFRACTION D_max: 120.9 Å Quality: EXCELLENT

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	1p3i
沉积日期 deposition_date	2003-04-17
结构标题 title	;Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants ;
关键词 keywords	Sin mutants, Nucleosome Core Particle, chromatin, protein/DNA interaction, STRUCTURAL PROTEIN-DNA COMPLEX; STRUCTURAL PROTEIN/DNA
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	39.99 Å
回转半径 Rg (电子) rg_electron	37.29 Å
零角强度 I(0) i0	823525000.00
分子量 molecular_weight	175440.0 kDa
排除体积 excluded_volume	194760 Å³
包络体积 envelope_volume	287600 Å³
水化壳体积 shell_volume	62538 Å³
包络直径 envelope_diameter	123.5 Å
壳层 Rg shell_rg	44.78 Å
包络 Rg envelope_rg	36.83 Å
形状 Rg shape_rg	37.13 Å
总 Rg total_rg	38.00 Å
总原子数 total_atoms	11970
残基数 n_residues	1048
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	120.9 Å
Rg (实空间) rg_real	39.73 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	8.2350e+08
I(0) 误差 (实空间) i0_real_error	1.5750e+07
Rg (倒空间) rg_reciprocal	39.90 Å
I(0) (倒空间) i0_reciprocal	823700000.0000
解质量估计 total_estimate	0.9078
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	45.3 Å
偏度 Skewness skewness	0.093
峰度 Kurtosis kurtosis	-0.692
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	71000000.0000
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: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.924

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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 (6)

Entity 1 polymer

描述 description	Palindromic 146bp Human Alpha-Satellite DNA fragment
分子量 formula_weight	45054.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	I,J
原子数 atom_count	12260

ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT

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

Entity 2 polymer

描述 description	Histone H3
分子量 formula_weight	15363.9 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,E

ARTKQTARKSTGGKAPRKQLATKAARKSAPATGESKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Histone H4
分子量 formula_weight	11244.2 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,F

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKHISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 4 polymer

描述 description	Histone H2A
分子量 formula_weight	13962.2 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	C,G

SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESAKSAKSK

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 5 polymer

描述 description	Histone H2B
分子量 formula_weight	13834.1 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	D,H

PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	African clawed frog
NCBI 分类编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 6 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	290

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1p3ia_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.22 — Histone-fold
超家族 Superfamily superfamily	a.22.1 — Histone-fold
家族 Family family	a.22.1.1 — Nucleosome core histones

结构域编号 domain_id	d1p3ib_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.22 — Histone-fold
超家族 Superfamily superfamily	a.22.1 — Histone-fold
家族 Family family	a.22.1.1 — Nucleosome core histones

结构域编号 domain_id	d1p3ic_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.22 — Histone-fold
超家族 Superfamily superfamily	a.22.1 — Histone-fold
家族 Family family	a.22.1.1 — Nucleosome core histones

结构域编号 domain_id	d1p3id_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.22 — Histone-fold
超家族 Superfamily superfamily	a.22.1 — Histone-fold
家族 Family family	a.22.1.1 — Nucleosome core histones

结构域编号 domain_id	d1p3ie_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.22 — Histone-fold
超家族 Superfamily superfamily	a.22.1 — Histone-fold
家族 Family family	a.22.1.1 — Nucleosome core histones

结构域编号 domain_id	d1p3if_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.22 — Histone-fold
超家族 Superfamily superfamily	a.22.1 — Histone-fold
家族 Family family	a.22.1.1 — Nucleosome core histones

结构域编号 domain_id	d1p3ig_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.22 — Histone-fold
超家族 Superfamily superfamily	a.22.1 — Histone-fold
家族 Family family	a.22.1.1 — Nucleosome core histones

结构域编号 domain_id	d1p3ih_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.22 — Histone-fold
超家族 Superfamily superfamily	a.22.1 — Histone-fold
家族 Family family	a.22.1.1 — Nucleosome core histones

CATH v4.4 (8 domains)

结构域编号 domain_id	1p3iA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	20 — Histone, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Histone, subunit A

结构域编号 domain_id	1p3iB00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	20 — Histone, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Histone, subunit A

结构域编号 domain_id	1p3iC00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	20 — Histone, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Histone, subunit A

结构域编号 domain_id	1p3iD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	20 — Histone, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Histone, subunit A

结构域编号 domain_id	1p3iE00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	20 — Histone, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Histone, subunit A

结构域编号 domain_id	1p3iF00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	20 — Histone, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Histone, subunit A

结构域编号 domain_id	1p3iG00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	20 — Histone, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Histone, subunit A

结构域编号 domain_id	1p3iH00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	20 — Histone, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Histone, subunit A

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7. 引用文献 (1)

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晶胞边长 a length_a	106.610 Å
晶胞边长 b length_b	109.752 Å
晶胞边长 c length_c	182.300 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	2.300 Å
最低分辨率 resolution_low	100.000 Å
R 因子 r_factor	—
R_work r_work	0.2420
R_free r_free	0.2750

fit	/app/data/saxs_computation/p3/1p3i/1p3i.fit
pddf	/app/data/pr_computation/p3/1p3i/1p3i.pr.out
profile	/app/data/saxs_computation/p3/1p3i/1p3i.dat

;Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants ;

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 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 polymer

聚合体 Polymer

来源 Source

Entity 6 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)