SAXSdb — 2ead

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2ead
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 in complex with substrate
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	40.20 Å
回转半径 Rg (电子) rg_electron	39.66 Å
零角强度 I(0) i0	588049000.00
分子量 molecular_weight	191790.0 kDa
排除体积 excluded_volume	236630 Å³
包络体积 envelope_volume	288420 Å³
水化壳体积 shell_volume	60121 Å³
包络直径 envelope_diameter	138.3 Å
壳层 Rg shell_rg	45.91 Å
包络 Rg envelope_rg	39.35 Å
形状 Rg shape_rg	39.65 Å
总 Rg total_rg	39.96 Å
总原子数 total_atoms	13525
残基数 n_residues	1770
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	131.6 Å
Rg (实空间) rg_real	40.23 Å
Rg 误差 (实空间) rg_real_error	1.45 Å
I(0) (实空间) i0_real	5.8800e+08
I(0) 误差 (实空间) i0_real_error	1.1330e+07
Rg (倒空间) rg_reciprocal	40.20 Å
I(0) (倒空间) i0_reciprocal	588000000.0000
解质量估计 total_estimate	0.8855
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	40.5 Å
偏度 Skewness skewness	0.325
峰度 Kurtosis kurtosis	-0.511
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	147900000.0000
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: 0.903; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.828

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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	96913.2 kDa
EC 编号 ec_number	3.2.1.63
突变 mutation	E566A
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	15308

MVIASVEDGGDGDTSKDDWLWYKQPASQTDATATAGGNYGNPDNNRWQQTTLPFGNGKIGGTVWGEVSRERVTFNEETLWTGGPGSSTSYNGGNNETKGQNGATLRALNKQLANGAETVNPGNLTGGENAAEQGNYLNWGDIYLDYGFNDTTVTEYRRDLNLSKGKADVTFKHDGVTYTREYFASNPDNVMVARLTASKAGKLNFNVSMPTNTNYSKTGETTTVKGDTLTVKGALGNNGLLYNSQIKVVLDNGEGTLSEGSDGASLKVSDAKAVTLYIAAATDYKQKYPSYRTGETAAEVNTRVAKVVQDAANKGYTAVKKAHIDDHSAIYDRVKIDLGQSGHSSDGAVATDALLKAYQRGSATTAQKRELETLVYKYGRYLTIGSSRENSQLPSNLQGIWSVTAGDNAHGNTPWGSDFHMNVNLQMNYWPTYSANMGELAEPLIEYVEGLVKPGRVTAKVYAGAETTNPETTPIGEGEGYMAHTENTAYGWTAPGQSFSWGWSPAAVPWILQNVYEAYEYSGDPALLDRVYALLKEESHFYVNYMLHKAGSSSGDRLTTGVAYSPAQGPLGTDGNTYESSLVWQMLNDAIEAAKAKGDPDGLVGNTTDCSADNWAKNDSGNFTDANANRSWSCAKSLLKPIEVGDSGQIKEWYFEGALGKKKDGSTISGYQADNQHRHMSHLLGLFPGDLITIDNSEYMDAAKTSLRYRCFKGNVLQSNTGWAIGQRINSWARTGDGNTTYQLVELQLKNAMYANLFDYHAPFQIDGNFGNTSGVDEMLLQSNSTFTDTAGKKYVNYTNILPALPDAWAGGSVSGLVARGNFTVGTTWKNGKATEVRLTSNKGKQAAVKITAGGAQNYEVKNGDTAVNAKVVTNADGASLLVFDTTAGTTYTITKKAS

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 branched

描述 description	alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
分子量 formula_weight	488.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 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	4

Entity 4 non-polymer

描述 description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
分子量 formula_weight	195.2 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	1783

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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	2eadA01
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	2eadA02
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	2eadA03
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	2eadB01
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	2eadB02
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	2eadB03
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	88.448 Å
晶胞边长 b length_b	72.743 Å
晶胞边长 c length_c	129.207 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.68 °
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	1.890 Å
最低分辨率 resolution_low	37.600 Å
R 因子 r_factor	0.1619
R_work r_work	0.1594
R_free r_free	0.2096

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

Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with substrate

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