2hcd

Crystal structure of the ligand binding domain of the Vitamin D nuclear receptor in complex with Gemini and a coactivator peptide

Method: X-RAY DIFFRACTION D_max: 62.4 Å Quality: GOOD

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	2hcd
沉积日期 deposition_date	2006-06-16
结构标题 title	Crystal structure of the ligand binding domain of the Vitamin D nuclear receptor in complex with Gemini and a coactivator peptide
关键词 keywords	alpha helical sandwich, GENE REGULATION; GENE REGULATION
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	19.26 Å
回转半径 Rg (电子) rg_electron	17.90 Å
零角强度 I(0) i0	13914400.00
分子量 molecular_weight	28903.0 kDa
排除体积 excluded_volume	36628 Å³
包络体积 envelope_volume	40856 Å³
水化壳体积 shell_volume	18923 Å³
包络直径 envelope_diameter	64.0 Å
壳层 Rg shell_rg	24.41 Å
包络 Rg envelope_rg	18.23 Å
形状 Rg shape_rg	17.88 Å
总 Rg total_rg	18.96 Å
总原子数 total_atoms	2031
残基数 n_residues	249
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	62.4 Å
Rg (实空间) rg_real	19.15 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	1.3910e+07
I(0) 误差 (实空间) i0_real_error	1.7470e+05
Rg (倒空间) rg_reciprocal	19.17 Å
I(0) (倒空间) i0_reciprocal	13910000.0000
解质量估计 total_estimate	0.8017
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	24.3 Å
偏度 Skewness skewness	0.214
峰度 Kurtosis kurtosis	-0.272
角度范围 angular_range	— – 0.4150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	2724000.0000
实空间数据点数 n_real_points	73
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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	Vitamin D receptor
分子量 formula_weight	34060.7 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
原子数 atom_count	2069

GSHMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	zebrafish
NCBI 分类编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	SRC-1 from Nuclear receptor coactivator 1
分子量 formula_weight	1776.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

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

RHKILHRLLQEGSPS

Entity 3 non-polymer

描述 description	21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E)
分子量 formula_weight	502.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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) 1 domains

CATH v4.4 (1 domains)

结构域编号 domain_id	2hcdA00
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	65.859 Å
晶胞边长 b length_b	65.859 Å
晶胞边长 c length_c	265.018 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 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2270
R_work r_work	0.2040
R_free r_free	0.2600

fit	/app/data/saxs_computation/hc/2hcd/2hcd.fit
pddf	/app/data/pr_computation/hc/2hcd/2hcd.pr.out
profile	/app/data/saxs_computation/hc/2hcd/2hcd.dat

Crystal structure of the ligand binding domain of the Vitamin D nuclear receptor in complex with Gemini and a coactivator peptide

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

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)