SAXSdb — 2hio

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hio
沉积日期 deposition_date	1999-06-15
结构标题 title	HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN
关键词 keywords	HISTONE, CHROMOSOMAL PROTEIN, STRUCTURAL PROTEIN, DNA BINDING PROTEIN; STRUCTURAL PROTEIN,DNA BINDING 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	24.84 Å
回转半径 Rg (电子) rg_electron	24.08 Å
零角强度 I(0) i0	27091700.00
分子量 molecular_weight	40480.0 kDa
排除体积 excluded_volume	51190 Å³
包络体积 envelope_volume	63555 Å³
水化壳体积 shell_volume	22588 Å³
包络直径 envelope_diameter	85.3 Å
壳层 Rg shell_rg	30.29 Å
包络 Rg envelope_rg	24.06 Å
形状 Rg shape_rg	24.03 Å
总 Rg total_rg	25.04 Å
总原子数 total_atoms	2850
残基数 n_residues	362
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	85.6 Å
Rg (实空间) rg_real	24.85 Å
Rg 误差 (实空间) rg_real_error	0.66 Å
I(0) (实空间) i0_real	2.7090e+07
I(0) 误差 (实空间) i0_real_error	4.0200e+05
Rg (倒空间) rg_reciprocal	24.85 Å
I(0) (倒空间) i0_reciprocal	27090000.0000
解质量估计 total_estimate	0.8760
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	25.8 Å
偏度 Skewness skewness	0.307
峰度 Kurtosis kurtosis	-0.495
角度范围 angular_range	— – 0.3200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	6214000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.997

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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	PROTEIN (HISTONE H2A)
分子量 formula_weight	13838.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2850

SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTDSHKAKAK

Entity 2 polymer

描述 description	PROTEIN (HISTONE H2B)
分子量 formula_weight	13822.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

PEPAKSAPAPKKGSKKAVTKTQKKGDKKRKKSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK

Entity 3 polymer

描述 description	PROTEIN (HISTONE H3)
分子量 formula_weight	15421.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Entity 4 polymer

描述 description	PROTEIN (HISTONE H4)
分子量 formula_weight	11466.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQERTLYGFGG

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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	d2hioa_
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	d2hiob_
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	d2hioc_
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	d2hiod_
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 (4 domains)

结构域编号 domain_id	2hioA00
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	2hioB00
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	2hioC00
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	2hioD00
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 (7)

The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix.

Proc.Natl.Acad.Sci.USA (1991)

PMID: 1946434 · DOI: 10.1073/pnas.88.22.10148 PRIMARY

Spectropolarimetric Analysis of the Core Histone Octamer and its Subunits

Biochemistry (1990)

Crystallographic Structure of the Octameric Histone Core of the Nucleosome at a Resolution of 3.3 A

Science (1985)

Crystals of the Octameric Histone Core of the Nucleosome

Science (1984)

Reversible Association of Calf Thymus Histones to Form the Symmetrical Octamer (H2Ah2Bh3H4)2: A Case of a Mixed-Associating System

Biochemistry (1980)

The Histone Core Complex: An Octamer Assembled by Two Sets of Protein-Protein Interactions

Biochemistry (1978)

The Compaction of DNA Helices Into Either Continuous Supercoils or Folded-Fiber Rods and Toroids

Cell(Cambridge,Mass.) (1978)

DOI: 10.1016/0092-8674(78)90198-8

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晶胞边长 a length_a	118.820 Å
晶胞边长 b length_b	118.820 Å
晶胞边长 c length_c	102.930 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	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.2550
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/hi/2hio/2hio.fit
pddf	/app/data/pr_computation/hi/2hio/2hio.pr.out
profile	/app/data/saxs_computation/hi/2hio/2hio.dat

HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN

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

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)