8gdm

;Crystal structure of human cellular retinol binding protein 1 in complex with {[3-(diphenylmethyl)-1,2,4-oxadiazol-5-yl]methyl}(methyl)[1-(thiophen-2-yl)ethyl]amine ;

Method: X-RAY DIFFRACTION D_max: 47.7 Å Quality: EXCELLENT

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	8gdm
沉积日期 deposition_date	2023-03-06
结构标题 title	;Crystal structure of human cellular retinol binding protein 1 in complex with {[3-(diphenylmethyl)-1,2,4-oxadiazol-5-yl]methyl}(methyl)[1-(thiophen-2-yl)ethyl]amine ;
关键词 keywords	RBP1, CRBP1, retinol-binding, retinol, vitamin A, Retinol-binding protein; Retinol-binding protein
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	15.62 Å
回转半径 Rg (电子) rg_electron	14.26 Å
零角强度 I(0) i0	5230210.00
分子量 molecular_weight	16400.0 kDa
排除体积 excluded_volume	20492 Å³
包络体积 envelope_volume	22838 Å³
水化壳体积 shell_volume	13409 Å³
包络直径 envelope_diameter	46.5 Å
壳层 Rg shell_rg	20.28 Å
包络 Rg envelope_rg	14.51 Å
形状 Rg shape_rg	14.26 Å
总 Rg total_rg	15.43 Å
总原子数 total_atoms	2253
残基数 n_residues	136
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	47.7 Å
Rg (实空间) rg_real	15.50 Å
Rg 误差 (实空间) rg_real_error	0.24 Å
I(0) (实空间) i0_real	5.2300e+06
I(0) 误差 (实空间) i0_real_error	6.1210e+04
Rg (倒空间) rg_reciprocal	15.51 Å
I(0) (倒空间) i0_reciprocal	5230000.0000
解质量估计 total_estimate	0.9012
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	19.9 Å
偏度 Skewness skewness	0.086
峰度 Kurtosis kurtosis	-0.444
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1092000.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.988

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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 (3)

Entity 1 polymer

描述 description	Retinol-binding protein 1
分子量 formula_weight	16700.1 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	2446

MPVDFTGYWKMLVNENFEEYLRALDVNVALRKIANLLKPDKEIVQDGDHMIIRTLSTFRNYIMDFQVGKEFEEDLTGIDDRKCMTTVSWDGDKLQCVQKGEKEGRGWTQWIEGDELHLEMRVEGVVCKQVFKKVQHHHHHH

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	Escherichia coli

Entity 2 non-polymer

描述 description	(1S)-N-{[3-(diphenylmethyl)-1,2,4-oxadiazol-5-yl]methyl}-N-methyl-1-(thiophen-2-yl)ethan-1-amine
分子量 formula_weight	389.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	152

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7. 引用文献 (1)

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晶胞边长 a length_a	37.349 Å
晶胞边长 b length_b	39.015 Å
晶胞边长 c length_c	94.027 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	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	36.040 Å
R 因子 r_factor	0.1850
R_work r_work	0.1833
R_free r_free	0.2134

fit	/app/data/saxs_computation/gd/8gdm/8gdm.fit
pddf	/app/data/pr_computation/gd/8gdm/8gdm.pr.out
profile	/app/data/saxs_computation/gd/8gdm/8gdm.dat

;Crystal structure of human cellular retinol binding protein 1 in complex with {[3-(diphenylmethyl)-1,2,4-oxadiazol-5-yl]methyl}(methyl)[1-(thiophen-2-yl)ethyl]amine ;

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