SAXSdb — 1isy

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1isy
沉积日期 deposition_date	2001-12-27
结构标题 title	Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with glucose
关键词 keywords	ALPHA-BETA BARREL, PROTEIN-SUGAR COMPLEX, CARBOHYDRATE BINDING DOMAIN, 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	31.75 Å
回转半径 Rg (电子) rg_electron	31.19 Å
零角强度 I(0) i0	160111000.00
分子量 molecular_weight	94214.0 kDa
排除体积 excluded_volume	114920 Å³
包络体积 envelope_volume	139870 Å³
水化壳体积 shell_volume	37393 Å³
包络直径 envelope_diameter	103.7 Å
壳层 Rg shell_rg	38.11 Å
包络 Rg envelope_rg	30.82 Å
形状 Rg shape_rg	31.16 Å
总 Rg total_rg	31.78 Å
总原子数 total_atoms	6624
残基数 n_residues	872
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	102.4 Å
Rg (实空间) rg_real	31.71 Å
Rg 误差 (实空间) rg_real_error	0.75 Å
I(0) (实空间) i0_real	1.6010e+08
I(0) 误差 (实空间) i0_real_error	2.5350e+06
Rg (倒空间) rg_reciprocal	31.73 Å
I(0) (倒空间) i0_reciprocal	160100000.0000
解质量估计 total_estimate	0.6819
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	36.9 Å
偏度 Skewness skewness	0.257
峰度 Kurtosis kurtosis	-0.530
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	46090000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.996; Smooth: 0.889

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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	endo-1,4-beta-D-xylanase
分子量 formula_weight	46791.2 kDa
EC 编号 ec_number	3.2.1.8
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	7294

AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVNEAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGGSSTPPPSGGGQIKGVGSGRCLDVPNASTTDGTQVQLYDCHSATNQQWTYTDAGELRVYGDKCLDAAGTGNGTKVQIYSCWGGDNQKWRLNSDGSIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT

来源 Source

来源生物 organism	Streptomyces olivaceoviridis
NCBI 分类编号 ncbi_taxonomy_id	1921
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	beta-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

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	661

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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	d1isya1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.2 — Ricin B-like lectins
家族 Family family	b.42.2.1 — Ricin B-like

结构域编号 domain_id	d1isya2
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.1.8.3 — beta-glycanases

结构域编号 domain_id	d1isyb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.42 — beta-Trefoil
超家族 Superfamily superfamily	b.42.2 — Ricin B-like lectins
家族 Family family	b.42.2.1 — Ricin B-like

结构域编号 domain_id	d1isyb2
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.1.8.3 — beta-glycanases

CATH v4.4 (4 domains)

结构域编号 domain_id	1isyA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1isyA02
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	1isyB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	80 — Trefoil
拓扑 Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	1isyB02
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 (3)

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晶胞边长 a length_a	75.250 Å
晶胞边长 b length_b	94.470 Å
晶胞边长 c length_c	138.350 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	8

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

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	29.820 Å
R 因子 r_factor	0.1910
R_work r_work	0.1910
R_free r_free	0.2350

fit	/app/data/saxs_computation/is/1isy/1isy.fit
pddf	/app/data/pr_computation/is/1isy/1isy.pr.out
profile	/app/data/saxs_computation/is/1isy/1isy.dat

Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with glucose

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