SAXSdb — 2eab

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2eab
沉积日期 deposition_date	2007-01-31
结构标题 title	Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum (apo form)
关键词 keywords	FUCOSIDASE, GLYCOSIDE HYDROLASE, 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	40.61 Å
回转半径 Rg (电子) rg_electron	40.38 Å
零角强度 I(0) i0	590569000.00
分子量 molecular_weight	192240.0 kDa
排除体积 excluded_volume	237230 Å³
包络体积 envelope_volume	292820 Å³
水化壳体积 shell_volume	60068 Å³
包络直径 envelope_diameter	144.7 Å
壳层 Rg shell_rg	46.07 Å
包络 Rg envelope_rg	40.08 Å
形状 Rg shape_rg	40.36 Å
总 Rg total_rg	40.71 Å
总原子数 total_atoms	13557
残基数 n_residues	1769
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	136.1 Å
Rg (实空间) rg_real	40.66 Å
Rg 误差 (实空间) rg_real_error	1.16 Å
I(0) (实空间) i0_real	5.9060e+08
I(0) 误差 (实空间) i0_real_error	1.0630e+07
Rg (倒空间) rg_reciprocal	40.61 Å
I(0) (倒空间) i0_reciprocal	590500000.0000
解质量估计 total_estimate	0.8805
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	41.9 Å
偏度 Skewness skewness	0.362
峰度 Kurtosis kurtosis	-0.425
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	165100000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.874

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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	Alpha-fucosidase
分子量 formula_weight	96971.2 kDa
EC 编号 ec_number	3.2.1.63
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	16940

MVIASVEDGGDGDTSKDDWLWYKQPASQTDATATAGGNYGNPDNNRWQQTTLPFGNGKIGGTVWGEVSRERVTFNEETLWTGGPGSSTSYNGGNNETKGQNGATLRALNKQLANGAETVNPGNLTGGENAAEQGNYLNWGDIYLDYGFNDTTVTEYRRDLNLSKGKADVTFKHDGVTYTREYFASNPDNVMVARLTASKAGKLNFNVSMPTNTNYSKTGETTTVKGDTLTVKGALGNNGLLYNSQIKVVLDNGEGTLSEGSDGASLKVSDAKAVTLYIAAATDYKQKYPSYRTGETAAEVNTRVAKVVQDAANKGYTAVKKAHIDDHSAIYDRVKIDLGQSGHSSDGAVATDALLKAYQRGSATTAQKRELETLVYKYGRYLTIGSSRENSQLPSNLQGIWSVTAGDNAHGNTPWGSDFHMNVNLQMNYWPTYSANMGELAEPLIEYVEGLVKPGRVTAKVYAGAETTNPETTPIGEGEGYMAHTENTAYGWTAPGQSFSWGWSPAAVPWILQNVYEAYEYSGDPALLDRVYALLKEESHFYVNYMLHKAGSSSGDRLTTGVAYSPEQGPLGTDGNTYESSLVWQMLNDAIEAAKAKGDPDGLVGNTTDCSADNWAKNDSGNFTDANANRSWSCAKSLLKPIEVGDSGQIKEWYFEGALGKKKDGSTISGYQADNQHRHMSHLLGLFPGDLITIDNSEYMDAAKTSLRYRCFKGNVLQSNTGWAIGQRINSWARTGDGNTTYQLVELQLKNAMYANLFDYHAPFQIDGNFGNTSGVDEMLLQSNSTFTDTAGKKYVNYTNILPALPDAWAGGSVSGLVARGNFTVGTTWKNGKATEVRLTSNKGKQAAVKITAGGAQNYEVKNGDTAVNAKVVTNADGASLLVFDTTAGTTYTITKKAS

来源 Source

来源生物 organism	Bifidobacterium bifidum
NCBI 分类编号 ncbi_taxonomy_id	1681
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 4 non-polymer

描述 description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	122.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	3383

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6. 折叠分类 (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

结构域编号 domain_id	2eabA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	50 — putative glycoside hydrolase family protein from bacillus halodurans

结构域编号 domain_id	2eabA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2eabA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

结构域编号 domain_id	2eabB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	50 — putative glycoside hydrolase family protein from bacillus halodurans

结构域编号 domain_id	2eabB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2eabB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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7. 引用文献 (1)

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晶胞边长 a length_a	90.183 Å
晶胞边长 b length_b	112.035 Å
晶胞边长 c length_c	98.317 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	94.74 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.120 Å
最低分辨率 resolution_low	35.050 Å
R 因子 r_factor	0.1760
R_work r_work	0.1750
R_free r_free	0.1890

fit	/app/data/saxs_computation/ea/2eab/2eab.fit
pddf	/app/data/pr_computation/ea/2eab/2eab.pr.out
profile	/app/data/saxs_computation/ea/2eab/2eab.dat

Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum (apo form)

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution