2h1o

Structure of FitAB bound to IR36 DNA fragment

Method: X-RAY DIFFRACTION D_max: 111.2 Å Quality: REASONABLE

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	2h1o
沉积日期 deposition_date	2006-05-16
结构标题 title	Structure of FitAB bound to IR36 DNA fragment
关键词 keywords	PIN domain, RHH protein, DNA binding, tetramer of dimers, GENE REGULATION-DNA COMPLEX COMPLEX; GENE REGULATION/DNA COMPLEX
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	36.77 Å
回转半径 Rg (电子) rg_electron	35.70 Å
零角强度 I(0) i0	245695000.00
分子量 molecular_weight	113140.0 kDa
排除体积 excluded_volume	136000 Å³
包络体积 envelope_volume	194230 Å³
水化壳体积 shell_volume	44541 Å³
包络直径 envelope_diameter	118.4 Å
壳层 Rg shell_rg	43.41 Å
包络 Rg envelope_rg	34.29 Å
形状 Rg shape_rg	35.70 Å
总 Rg total_rg	36.21 Å
总原子数 total_atoms	7860
残基数 n_residues	898
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	111.2 Å
Rg (实空间) rg_real	36.54 Å
Rg 误差 (实空间) rg_real_error	0.90 Å
I(0) (实空间) i0_real	2.4570e+08
I(0) 误差 (实空间) i0_real_error	4.0890e+06
Rg (倒空间) rg_reciprocal	36.69 Å
I(0) (倒空间) i0_reciprocal	245700000.0000
解质量估计 total_estimate	0.7106
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	51.7 Å
偏度 Skewness skewness	0.001
峰度 Kurtosis kurtosis	-0.613
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13510000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.995; Smooth: 0.897

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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 (5)

Entity 1 polymer

描述 description	IR36-strand 1
分子量 formula_weight	11170.0 kDa
突变 mutation	iodo
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	U
原子数 atom_count	7906

AGATTGCTATCATTTTTTTTATTTTGATAGCATUTG

Entity 2 polymer

描述 description	IR36-strand 2
分子量 formula_weight	11198.1 kDa
突变 mutation	iodo
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	V

CAAATGCTATCAAAAUAAAAAAAATGATAGCAATCT

Entity 3 polymer

描述 description	Trafficking protein B
分子量 formula_weight	15919.3 kDa
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	A,B,C,D

MILLDTNVISEPLRPQPNERVVAWLDSLILEDVYLSAITVAEMRLGVALLLNGKKKNVLHERMEQSILPLFAGRILPFDEPVAAIYAQIRSYAKTHGKEIAAADGYIAATAKQHSMTVATRDTGSFFAADVAVFNPWHLEHHH

来源 Source

来源生物 organism	Neisseria gonorrhoeae
NCBI 分类编号 ncbi_taxonomy_id	485
宿主生物 host_organism	Escherichia coli BL21

Entity 4 polymer

描述 description	Trafficking protein A
分子量 formula_weight	7283.3 kDa
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	E,F,G,H

ASVVIRNLSEATHNAIKFRARAAGRSTEAEIRLILDNIAKAQQTVRLGSMLASIGQEIGGVELEDVRG

来源 Source

来源生物 organism	Neisseria gonorrhoeae
NCBI 分类编号 ncbi_taxonomy_id	485
宿主生物 host_organism	Escherichia coli BL21

Entity 5 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	46

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6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d2h1oa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.120 — PIN domain-like
超家族 Superfamily superfamily	c.120.1 — PIN domain-like
家族 Family family	c.120.1.1 — PIN domain

结构域编号 domain_id	d2h1oa2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2h1ob1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.120 — PIN domain-like
超家族 Superfamily superfamily	c.120.1 — PIN domain-like
家族 Family family	c.120.1.1 — PIN domain

结构域编号 domain_id	d2h1ob2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2h1oc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.120 — PIN domain-like
超家族 Superfamily superfamily	c.120.1 — PIN domain-like
家族 Family family	c.120.1.1 — PIN domain

结构域编号 domain_id	d2h1oc2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2h1od1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.120 — PIN domain-like
超家族 Superfamily superfamily	c.120.1 — PIN domain-like
家族 Family family	c.120.1.1 — PIN domain

结构域编号 domain_id	d2h1od2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d2h1oe1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.8 — Trafficking protein A-like

结构域编号 domain_id	d2h1of1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.8 — Trafficking protein A-like

结构域编号 domain_id	d2h1og1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.8 — Trafficking protein A-like

结构域编号 domain_id	d2h1oh1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.43 — Ribbon-helix-helix
超家族 Superfamily superfamily	a.43.1 — Ribbon-helix-helix
家族 Family family	a.43.1.8 — Trafficking protein A-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2h1oA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1010 — 5'-nuclease

结构域编号 domain_id	2h1oB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1010 — 5'-nuclease

结构域编号 domain_id	2h1oC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1010 — 5'-nuclease

结构域编号 domain_id	2h1oD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1010 — 5'-nuclease

结构域编号 domain_id	2h1oE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1220 — Arc Repressor Mutant
同源超家族 H-superfamily homologous superfamily	10 — Met repressor-like

结构域编号 domain_id	2h1oF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1220 — Arc Repressor Mutant
同源超家族 H-superfamily homologous superfamily	10 — Met repressor-like

结构域编号 domain_id	2h1oG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1220 — Arc Repressor Mutant
同源超家族 H-superfamily homologous superfamily	10 — Met repressor-like

结构域编号 domain_id	2h1oH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1220 — Arc Repressor Mutant
同源超家族 H-superfamily homologous superfamily	10 — Met repressor-like

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7. 引用文献 (1)

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晶胞边长 a length_a	75.040 Å
晶胞边长 b length_b	82.403 Å
晶胞边长 c length_c	135.503 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.19 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	70.360 Å
R 因子 r_factor	0.2690
R_work r_work	0.2120
R_free r_free	0.2690

fit	/app/data/saxs_computation/h1/2h1o/2h1o.fit
pddf	/app/data/pr_computation/h1/2h1o/2h1o.pr.out
profile	/app/data/saxs_computation/h1/2h1o/2h1o.dat

Structure of FitAB bound to IR36 DNA fragment

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 (5)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 water

6. 折叠分类 (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)