1m1a

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

Method: X-RAY DIFFRACTION D_max: 118.6 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	1m1a
沉积日期 deposition_date	2002-06-18
结构标题 title	LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
关键词 keywords	nucleosome, chromatin, histone, pyrrole-imidazole polyamide, DNA regognition, chromatin remodeling, 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	39.92 Å
回转半径 Rg (电子) rg_electron	37.34 Å
零角强度 I(0) i0	846846000.00
分子量 molecular_weight	178490.0 kDa
排除体积 excluded_volume	198290 Å³
包络体积 envelope_volume	292020 Å³
水化壳体积 shell_volume	63183 Å³
包络直径 envelope_diameter	118.1 Å
壳层 Rg shell_rg	45.24 Å
包络 Rg envelope_rg	36.86 Å
形状 Rg shape_rg	37.18 Å
总 Rg total_rg	38.06 Å
总原子数 total_atoms	12158
残基数 n_residues	1059
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	118.6 Å
Rg (实空间) rg_real	39.75 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	8.4680e+08
I(0) 误差 (实空间) i0_real_error	1.4680e+07
Rg (倒空间) rg_reciprocal	39.92 Å
I(0) (倒空间) i0_reciprocal	847000000.0000
解质量估计 total_estimate	0.9056
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	47.4 Å
偏度 Skewness skewness	0.077
峰度 Kurtosis kurtosis	-0.707
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	66780000.0000
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: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.859

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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 (12)

Entity 1 polymer

描述 description	Palindromic 146 Base Pair DNA Fragment
分子量 formula_weight	45054.8 kDa
来源方法 src_method	syn
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	12378

ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT

Entity 2 polymer

描述 description	Histone H3.3C
分子量 formula_weight	15320.0 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

ARTKQTARKSTGGKAPRKQLVTKAAKKCAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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	11263.2 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

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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 type 1
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	13848.1 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

PEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

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 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 7 non-polymer

描述 description	4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID
分子量 formula_weight	141.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 8 non-polymer

描述 description	4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID
分子量 formula_weight	140.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 9 non-polymer

描述 description	GAMMA-AMINO-BUTANOIC ACID
分子量 formula_weight	103.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 10 non-polymer

描述 description	BETA-ALANINE
分子量 formula_weight	89.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 11 non-polymer

描述 description	3-AMINO-(DIMETHYLPROPYLAMINE)
分子量 formula_weight	102.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 12 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	220

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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	d1m1aa_
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	d1m1ab_
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	d1m1ac_
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	d1m1ad_
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	d1m1ae_
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	d1m1af_
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	d1m1ag_
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	d1m1ah_
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	1m1aA00
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	1m1aB00
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	1m1aC00
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	1m1aD00
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	1m1aE00
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	1m1aF00
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	1m1aG00
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	1m1aH00
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	106.719 Å
晶胞边长 b length_b	109.196 Å
晶胞边长 c length_c	177.353 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	2.650 Å
最低分辨率 resolution_low	60.000 Å
R 因子 r_factor	—
R_work r_work	0.2226
R_free r_free	0.2670

fit	/app/data/saxs_computation/m1/1m1a/1m1a.fit
pddf	/app/data/pr_computation/m1/1m1a/1m1a.pr.out
profile	/app/data/saxs_computation/m1/1m1a/1m1a.dat

LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA

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 (12)

Entity 1 polymer

聚合体 Polymer

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 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 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)