SAXSdb — 1tl8

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1tl8
沉积日期 deposition_date	2004-06-09
结构标题 title	;Human DNA topoisomerase I (70 kDa) in complex with the indenoisoquinoline AI-III-52 and covalent complex with a 22 base pair DNA duplex ;
关键词 keywords	COMPLEX (ISOMERASE-DNA), DNA, TOPOISOMERASE I, DRUG, POISON, IDENOISOQUINOLINE, ISOMERASE-DNA complex; ISOMERASE/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	28.87 Å
回转半径 Rg (电子) rg_electron	28.81 Å
零角强度 I(0) i0	125021000.00
分子量 molecular_weight	80656.0 kDa
排除体积 excluded_volume	97738 Å³
包络体积 envelope_volume	131570 Å³
水化壳体积 shell_volume	38251 Å³
包络直径 envelope_diameter	106.9 Å
壳层 Rg shell_rg	35.65 Å
包络 Rg envelope_rg	29.33 Å
形状 Rg shape_rg	28.77 Å
总 Rg total_rg	29.51 Å
总原子数 total_atoms	5619
残基数 n_residues	607
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	102.8 Å
Rg (实空间) rg_real	28.86 Å
Rg 误差 (实空间) rg_real_error	0.83 Å
I(0) (实空间) i0_real	1.2500e+08
I(0) 误差 (实空间) i0_real_error	2.0400e+06
Rg (倒空间) rg_reciprocal	28.86 Å
I(0) (倒空间) i0_reciprocal	125000000.0000
解质量估计 total_estimate	0.6317
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	35.5 Å
偏度 Skewness skewness	0.423
峰度 Kurtosis kurtosis	0.014
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20190000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.697; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.953; Smooth: 0.977

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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	5'-D(APAPAPAPAPGPAPCPTPT)-3'
分子量 formula_weight	3061.1 kDa
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	B
原子数 atom_count	5619

AAAAAGACTT

Entity 2 polymer

描述 description	5'-D((TPC)PGPAPAPAPAPAPTPTPTPTPT)-3'
分子量 formula_weight	3676.5 kDa
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	C

CGAAAAATTTTT

Entity 3 polymer

描述 description	5'-D(APAPAPAPAPTPTPTPTPTPCPGPAPAPGPTPCPTPTPTPTPT)-3'
分子量 formula_weight	6730.4 kDa
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	D

AAAAATTTTTCGAAGTCTTTTT

Entity 4 polymer

描述 description	DNA topoisomerase I
分子量 formula_weight	70248.0 kDa
EC 编号 ec_number	5.99.1.2
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF

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	Spodoptera frugiperda

Entity 5 non-polymer

描述 description	2,3-DIMETHOXY-12H-[1,3]DIOXOLO[5,6]INDENO[1,2-C]ISOQUINOLIN-6-IUM
分子量 formula_weight	322.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1tl8a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.2 — Long alpha-hairpin
超家族 Superfamily superfamily	a.2.8 — Eukaryotic DNA topoisomerase I, dispensable insert domain
家族 Family family	a.2.8.1 — Eukaryotic DNA topoisomerase I, dispensable insert domain

结构域编号 domain_id	d1tl8a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.163 — DNA breaking-rejoining enzymes
超家族 Superfamily superfamily	d.163.1 — DNA breaking-rejoining enzymes
家族 Family family	d.163.1.2 — Eukaryotic DNA topoisomerase I, catalytic core

结构域编号 domain_id	d1tl8a3
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.15 — Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
超家族 Superfamily superfamily	e.15.1 — Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
家族 Family family	e.15.1.1 — Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment

CATH v4.4 (4 domains)

结构域编号 domain_id	1tl8A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	11 — DNA Topoisomerase I; domain 2
同源超家族 H-superfamily homologous superfamily	10 — DNA Topoisomerase I, domain 2

结构域编号 domain_id	1tl8A02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	41 — Yeast DNA topoisomerase - domain 1

结构域编号 domain_id	1tl8A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	15 — Topoisomerase I; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Topoisomerase I; Chain A, domain 3

结构域编号 domain_id	1tl8A04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	132 — Topoisomerase I; Chain A, domain 4
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	56.949 Å
晶胞边长 b length_b	114.141 Å
晶胞边长 c length_c	73.499 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.18 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

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	3.100 Å
最低分辨率 resolution_low	46.570 Å
R 因子 r_factor	—
R_work r_work	0.2290
R_free r_free	0.3050

fit	/app/data/saxs_computation/tl/1tl8/1tl8.fit
pddf	/app/data/pr_computation/tl/1tl8/1tl8.pr.out
profile	/app/data/saxs_computation/tl/1tl8/1tl8.dat

;Human DNA topoisomerase I (70 kDa) in complex with the indenoisoquinoline AI-III-52 and covalent complex with a 22 base pair DNA duplex ;

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

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 non-polymer

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)