SAXSdb — 1nou

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1nou
沉积日期 deposition_date	2003-01-16
结构标题 title	Native human lysosomal beta-hexosaminidase isoform B
关键词 keywords	(beta/alpha)8-barrel, homodimer, family 20 glycosidase, 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	33.05 Å
回转半径 Rg (电子) rg_electron	32.20 Å
零角强度 I(0) i0	179814000.00
分子量 molecular_weight	110800.0 kDa
排除体积 excluded_volume	139830 Å³
包络体积 envelope_volume	170500 Å³
水化壳体积 shell_volume	42938 Å³
包络直径 envelope_diameter	110.0 Å
壳层 Rg shell_rg	40.06 Å
包络 Rg envelope_rg	32.27 Å
形状 Rg shape_rg	32.17 Å
总 Rg total_rg	32.91 Å
总原子数 total_atoms	7835
残基数 n_residues	960
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	104.1 Å
Rg (实空间) rg_real	32.96 Å
Rg 误差 (实空间) rg_real_error	0.53 Å
I(0) (实空间) i0_real	1.7980e+08
I(0) 误差 (实空间) i0_real_error	2.4340e+06
Rg (倒空间) rg_reciprocal	33.00 Å
I(0) (倒空间) i0_reciprocal	179800000.0000
解质量估计 total_estimate	0.9095
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	39.0 Å
偏度 Skewness skewness	0.222
峰度 Kurtosis kurtosis	-0.528
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	52670000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.977

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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	beta-hexosaminidase beta chain
分子量 formula_weight	58184.9 kDa
EC 编号 ec_number	3.2.1.52
来源方法 src_method	nat
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	8061

AKPGPALWPLPLSVKMTPNLLHLAPENFYISHSPNSTAGPSCTLLEEAFRRYHGYIFGFYKWHHEPAEFQAKTQVQQLLVSITLQSECDAFPNISSDESYTLLVKEPVAVLKANRVWGALRGLETFSQLVYQDSYGTFTINESTIIDSPRFSHRGILIDTSRHYLPVKIILKTLDAMAFNKFNVLHWHIVDDQSFPYQSITFPELSNKGSYSLSHVYTPNDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKDLLTPCYSRQNKLDSFGPINPTLNTTYSFLTTFFKEISEVFPDQFIHLGGDEVEFKCWESNPKIQDFMRQKGFGTDFKKLESFYIQKVLDIIATINKGSIVWQEVFDDKAKLAPGTIVEVWKDSAYPEELSRVTASGFPVILSAPWYLDLISYGQDWRKYYKVEPLDFGGTQKQKQLFIGGEACLWGEYVDATNLTPRLWPRASAVGERLWSSKDVRDMDDAYDRLTRHRCRMVERGIAAQPLYAGYCNHENM

Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 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	226

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1noua1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.6 — beta-N-acetylhexosaminidase catalytic domain

结构域编号 domain_id	d1noua2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.2 — beta-N-acetylhexosaminidase-like domain
家族 Family family	d.92.2.1 — beta-N-acetylhexosaminidase domain

结构域编号 domain_id	d1noub1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.6 — beta-N-acetylhexosaminidase catalytic domain

结构域编号 domain_id	d1noub2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.2 — beta-N-acetylhexosaminidase-like domain
家族 Family family	d.92.2.1 — beta-N-acetylhexosaminidase domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1nouA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	379 — Chitobiase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Chitobiase/beta-hexosaminidase domain 2-like

结构域编号 domain_id	1nouA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	1nouB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	379 — Chitobiase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Chitobiase/beta-hexosaminidase domain 2-like

结构域编号 domain_id	1nouB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

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7. 引用文献 (1)

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晶胞边长 a length_a	112.465 Å
晶胞边长 b length_b	112.465 Å
晶胞边长 c length_c	397.867 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	24

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	34.710 Å
R 因子 r_factor	0.2027
R_work r_work	0.2011
R_free r_free	0.2312

fit	/app/data/saxs_computation/no/1nou/1nou.fit
pddf	/app/data/pr_computation/no/1nou/1nou.pr.out
profile	/app/data/saxs_computation/no/1nou/1nou.dat

Native human lysosomal beta-hexosaminidase isoform B

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