9av4

;Design and application of synthetic 17B-HSD13 substrates to drug discovery, and to reveal preserved catalytic activity of protective human variants ;

Method: X-RAY DIFFRACTION D_max: 81.4 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	9av4
沉积日期 deposition_date	2024-03-01
结构标题 title	;Design and application of synthetic 17B-HSD13 substrates to drug discovery, and to reveal preserved catalytic activity of protective human variants ;
关键词 keywords	enzyme, substrate, HSd17B13, HYDROLASE; HYDROLASE
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	24.28 Å
回转半径 Rg (电子) rg_electron	23.51 Å
零角强度 I(0) i0	102653000.00
分子量 molecular_weight	53792.0 kDa
排除体积 excluded_volume	52350 Å³
包络体积 envelope_volume	85716 Å³
水化壳体积 shell_volume	29692 Å³
包络直径 envelope_diameter	81.1 Å
壳层 Rg shell_rg	31.49 Å
包络 Rg envelope_rg	23.96 Å
形状 Rg shape_rg	23.52 Å
总 Rg total_rg	24.15 Å
总原子数 total_atoms	4086
残基数 n_residues	503
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	81.4 Å
Rg (实空间) rg_real	24.26 Å
Rg 误差 (实空间) rg_real_error	0.40 Å
I(0) (实空间) i0_real	1.0270e+08
I(0) 误差 (实空间) i0_real_error	1.2610e+06
Rg (倒空间) rg_reciprocal	24.26 Å
I(0) (倒空间) i0_reciprocal	102700000.0000
解质量估计 total_estimate	0.8769
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	27.1 Å
偏度 Skewness skewness	0.367
峰度 Kurtosis kurtosis	-0.312
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	31280000.0000
实空间数据点数 n_real_points	64
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: 0.979; Smooth: 0.995

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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	Hydroxysteroid 17-beta dehydrogenase 13
分子量 formula_weight	35350.1 kDa
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	4153

MGNIILDLLLLLLTIIYSYLEALVKVFFPRKRKSVAGEIVLITGAGHGIGRWTAYEFAKQKSRLVLWDINKHGVEETAAECRKLGATVHTFVVDCGNREDIYNSVKQVKKEVGDVTILVNNAGTVYPADLLSTKDEEITKTFEINILGHFWITKALLPSMIKRNHGHIVTVASVCGHEGIPYLIPYCSSKFAAVGFHRALTLELQALGITGIKTSCLCPVFVNTGFTKNPSTRLWPILETDTVARSLIDGILTNKKMIFVPSYYNIYLILDKFLPERALAAINHLQNIQFEAVVGHKTRMKGSGHHHHHHHHHHH

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	Insect BA phytoplasma

Entity 2 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	4-(3,4-dichlorobenzene-1-sulfonamido)-2-fluorobenzoic acid
分子量 formula_weight	364.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	56

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7. 引用文献 (1)

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晶胞边长 a length_a	186.970 Å
晶胞边长 b length_b	76.060 Å
晶胞边长 c length_c	65.240 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.69 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.090 Å
最低分辨率 resolution_low	33.470 Å
R 因子 r_factor	0.2126
R_work r_work	0.2113
R_free r_free	0.2393

fit	/app/data/saxs_computation/av/9av4/9av4.fit
pddf	/app/data/pr_computation/av/9av4/9av4.pr.out
profile	/app/data/saxs_computation/av/9av4/9av4.dat

;Design and application of synthetic 17B-HSD13 substrates to drug discovery, and to reveal preserved catalytic activity of protective human variants ;

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