SAXSdb — 1r1k

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r1k
沉积日期 deposition_date	2003-09-24
结构标题 title	Crystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to ponasterone A
关键词 keywords	;NUCLEAR RECEPTOR, TRANSCRIPTION REGULATION, HETERODIMER, ALPHA-HELICAL SANDWICH, Structural Proteomics in Europe, SPINE, Structural Genomics, hormone-growth factor receptor COMPLEX ;; hormone/growth factor receptor
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	24.14 Å
回转半径 Rg (电子) rg_electron	22.75 Å
零角强度 I(0) i0	47214800.00
分子量 molecular_weight	55297.0 kDa
排除体积 excluded_volume	70159 Å³
包络体积 envelope_volume	82611 Å³
水化壳体积 shell_volume	29280 Å³
包络直径 envelope_diameter	74.2 Å
壳层 Rg shell_rg	30.48 Å
包络 Rg envelope_rg	22.91 Å
形状 Rg shape_rg	22.76 Å
总 Rg total_rg	23.62 Å
总原子数 total_atoms	3879
残基数 n_residues	477
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	73.0 Å
Rg (实空间) rg_real	23.96 Å
Rg 误差 (实空间) rg_real_error	0.34 Å
I(0) (实空间) i0_real	4.7210e+07
I(0) 误差 (实空间) i0_real_error	5.6930e+05
Rg (倒空间) rg_reciprocal	24.00 Å
I(0) (倒空间) i0_reciprocal	47220000.0000
解质量估计 total_estimate	0.9077
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	30.8 Å
偏度 Skewness skewness	0.111
峰度 Kurtosis kurtosis	-0.514
角度范围 angular_range	— – 0.3300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9285000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.998

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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	Ecdysone receptor
分子量 formula_weight	30369.0 kDa
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	D
原子数 atom_count	3887

GSHMASMTGGQQMGRDPLKNVPPLTANQKSLIARLVWYQEGYEQPSEEDLKRVTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFSDRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKNRKLPPFLEEIWDVADVA

来源 Source

来源生物 organism	Heliothis virescens
通用名 common_name	tobacco budworm
NCBI 分类编号 ncbi_taxonomy_id	7102
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	ULTRASPIRACLE PROTEIN
分子量 formula_weight	29951.8 kDa
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

MVQELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNHAPPIDTNMM

来源 Source

来源生物 organism	Heliothis virescens
通用名 common_name	tobacco budworm
NCBI 分类编号 ncbi_taxonomy_id	7102
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

描述 description	2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE
分子量 formula_weight	464.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
分子量 formula_weight	709.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	8

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1r1ka_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.123 — Nuclear receptor ligand-binding domain
超家族 Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
家族 Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

结构域编号 domain_id	d1r1kd_
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.123 — Nuclear receptor ligand-binding domain
超家族 Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
家族 Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (2 domains)

结构域编号 domain_id	1r1kA00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	565 — Retinoid X Receptor
同源超家族 H-superfamily homologous superfamily	10 — Retinoid X Receptor

结构域编号 domain_id	1r1kD00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	565 — Retinoid X Receptor
同源超家族 H-superfamily homologous superfamily	10 — Retinoid X Receptor

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7. 引用文献 (1)

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晶胞边长 a length_a	57.401 Å
晶胞边长 b length_b	57.401 Å
晶胞边长 c length_c	302.696 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	6

空间群 space_group	P 31 2 1
空间群编号 int_tables_number	152
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.3040

fit	/app/data/saxs_computation/r1/1r1k/1r1k.fit
pddf	/app/data/pr_computation/r1/1r1k/1r1k.pr.out
profile	/app/data/saxs_computation/r1/1r1k/1r1k.dat

Crystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to ponasterone A

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

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)