SAXSdb — 2gai

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gai
沉积日期 deposition_date	2006-03-08
结构标题 title	Structure of Full Length Topoisomerase I from Thermotoga maritima in triclinic crystal form
关键词 keywords	Topoisomerase, Zinc ribbon, ISOMERASE; ISOMERASE
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	41.55 Å
回转半径 Rg (电子) rg_electron	41.55 Å
零角强度 I(0) i0	250629000.00
分子量 molecular_weight	133870.0 kDa
排除体积 excluded_volume	169730 Å³
包络体积 envelope_volume	234920 Å³
水化壳体积 shell_volume	49526 Å³
包络直径 envelope_diameter	140.8 Å
壳层 Rg shell_rg	44.89 Å
包络 Rg envelope_rg	40.61 Å
形状 Rg shape_rg	41.51 Å
总 Rg total_rg	41.88 Å
总原子数 total_atoms	9428
残基数 n_residues	1162
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	140.2 Å
Rg (实空间) rg_real	43.39 Å
Rg 误差 (实空间) rg_real_error	0.57 Å
I(0) (实空间) i0_real	2.5040e+08
I(0) 误差 (实空间) i0_real_error	3.8660e+06
Rg (倒空间) rg_reciprocal	41.55 Å
I(0) (倒空间) i0_reciprocal	250600000.0000
解质量估计 total_estimate	0.6714
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	40.6 Å
偏度 Skewness skewness	0.450
峰度 Kurtosis kurtosis	-0.479
角度范围 angular_range	— – 0.1900 Å⁻¹
当前正则化参数 α current_alpha	2.2430
最高正则化参数 α highest_alpha	26350000.0000
实空间数据点数 n_real_points	39
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 0.888; Sysdev: 0.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.538

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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 (2)

Entity 1 polymer

描述 description	DNA topoisomerase I
分子量 formula_weight	72806.9 kDa
EC 编号 ec_number	5.99.1.2
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,B
原子数 atom_count	10600

MAKKVKKYIVVESPAKAKTIKSILGNEYEVFASMGHIIDLPKSKFGVDLEKDFEPEFAVIKGKEKVVEKLKDLAKKGELLIASDMDREGEAIAWHIARVTNTLGRKNRIVFSEITPRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFKSNLSAGRVQSATLKLVCDREREILRFVPKKYHRITVNFDGLTAEIDVKEKKFFDAETLKEIQSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLYEGVETKDGHIAFITYMRTDSTRVSDYAKEEARNLITEVFGEEYVGSKRERRKSNAKIQDAHEAIRPTNVFMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDGKYRFKGTVLKKIFDGYEKVWKTERNTGEFPFEEGESVKPVVVKIEEQETKPKPRYTEGSLVKEMERLGIGRPSTYASTIKLLLNRGYIKKIRGYLYPTIVGSVVMDYLEKKYSDVVSVSFTAEMEKDLDEVEQGKKTDKIVLREFYESFSSVFDRNDRIVVDFPTNQKCSCGKEMRLSFGKYGFYLKCECGKTRSVKNDEIAVIDDGKIFLGRKDSESGSPDGRSVEGKGNLSEKRRKGKKGS

来源 Source

来源生物 organism	Thermotoga maritima
NCBI 分类编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	1054

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	2gaiA01
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	140 —

结构域编号 domain_id	2gaiA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	460 — Topoisomerase I; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Topoisomerase I, domain 2

结构域编号 domain_id	2gaiA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	20 — Topoisomerase I; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Topoisomerase I, domain 3

结构域编号 domain_id	2gaiA04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	290 — Topoisomerase I; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Topoisomerase I, domain 4

结构域编号 domain_id	2gaiB01
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	140 —

结构域编号 domain_id	2gaiB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	460 — Topoisomerase I; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Topoisomerase I, domain 2

结构域编号 domain_id	2gaiB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	20 — Topoisomerase I; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Topoisomerase I, domain 3

结构域编号 domain_id	2gaiB04
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	290 — Topoisomerase I; domain 4
同源超家族 H-superfamily homologous superfamily	10 — Topoisomerase I, domain 4

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7. 引用文献 (1)

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晶胞边长 a length_a	45.118 Å
晶胞边长 b length_b	95.421 Å
晶胞边长 c length_c	96.508 Å
晶胞夹角 α angle_alpha	83.40 °
晶胞夹角 β angle_beta	86.15 °
晶胞夹角 γ angle_gamma	84.87 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	41.560 Å
R 因子 r_factor	0.1990
R_work r_work	0.1970
R_free r_free	0.2320

fit	/app/data/saxs_computation/ga/2gai/2gai.fit
pddf	/app/data/pr_computation/ga/2gai/2gai.pr.out
profile	/app/data/saxs_computation/ga/2gai/2gai.dat

Structure of Full Length Topoisomerase I from Thermotoga maritima in triclinic crystal form

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