SAXSdb — 2byk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2byk
沉积日期 deposition_date	2005-08-03
结构标题 title	Histone fold heterodimer of the Chromatin Accessibility Complex
关键词 keywords	CHRAC-14, NUCLEOSOME SLIDING, HISTONE FOLD, CHRAC-16, DNA-BINDING PROTEIN, DNA BINDING 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	21.68 Å
回转半径 Rg (电子) rg_electron	20.18 Å
零角强度 I(0) i0	20905600.00
分子量 molecular_weight	35265.0 kDa
排除体积 excluded_volume	44502 Å³
包络体积 envelope_volume	53195 Å³
水化壳体积 shell_volume	21891 Å³
包络直径 envelope_diameter	71.5 Å
壳层 Rg shell_rg	26.75 Å
包络 Rg envelope_rg	20.47 Å
形状 Rg shape_rg	20.18 Å
总 Rg total_rg	21.10 Å
总原子数 total_atoms	2480
残基数 n_residues	319
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	68.9 Å
Rg (实空间) rg_real	21.56 Å
Rg 误差 (实空间) rg_real_error	0.36 Å
I(0) (实空间) i0_real	2.0910e+07
I(0) 误差 (实空间) i0_real_error	2.5510e+05
Rg (倒空间) rg_reciprocal	21.58 Å
I(0) (倒空间) i0_reciprocal	20910000.0000
解质量估计 total_estimate	0.7181
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	26.7 Å
偏度 Skewness skewness	0.165
峰度 Kurtosis kurtosis	-0.456
角度范围 angular_range	— – 0.3650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4204000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 0.207; Positv: 1.000; Valcen: 1.000; Smooth: 0.987

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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	CHRAC-16
分子量 formula_weight	16020.7 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,C
原子数 atom_count	2518

MGEPRSQPPVERPPTAETFLPLSRVRTIMKSSMDTGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQKIRVHQFQEMLRLNRSAGSDDDDDDDDDDDEEESESESESDE

来源 Source

来源生物 organism	DROSOPHILA MELANOGASTER
通用名 common_name	FRUIT FLY
NCBI 分类编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	CHRAC-14
分子量 formula_weight	13862.6 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,D

MVERIEDLNLPNAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVKEKKESKASKKDSNTAENANASATATAEEAPE

来源 Source

来源生物 organism	DROSOPHILA MELANOGASTER
通用名 common_name	FRUIT FLY
NCBI 分类编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	38

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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	d2byka1
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.22.1.3 — TBP-associated factors, TAFs

结构域编号 domain_id	d2bykb1
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.22.1.3 — TBP-associated factors, TAFs

结构域编号 domain_id	d2bykc_
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.22.1.3 — TBP-associated factors, TAFs

结构域编号 domain_id	d2bykd_
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.22.1.3 — TBP-associated factors, TAFs

CATH v4.4 (4 domains)

结构域编号 domain_id	2bykA00
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	2bykB00
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	2bykC00
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	2bykD00
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	76.010 Å
晶胞边长 b length_b	76.010 Å
晶胞边长 c length_c	166.080 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	12

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	2.400 Å
最低分辨率 resolution_low	23.830 Å
R 因子 r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2780

fit	/app/data/saxs_computation/by/2byk/2byk.fit
pddf	/app/data/pr_computation/by/2byk/2byk.pr.out
profile	/app/data/saxs_computation/by/2byk/2byk.dat

Histone fold heterodimer of the Chromatin Accessibility Complex

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 polymer

聚合体 Polymer

来源 Source

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)