1uhv

Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase

Method: X-RAY DIFFRACTION D_max: 115.2 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	1uhv
沉积日期 deposition_date	2003-07-11
结构标题 title	Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase
关键词 keywords	family 39 glycoside hydrolase, xylosidase, xylan, xylose, covalent glycosyl-enzyme intermediate, 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	39.10 Å
回转半径 Rg (电子) rg_electron	37.96 Å
零角强度 I(0) i0	770126000.00
分子量 molecular_weight	235070.0 kDa
排除体积 excluded_volume	296180 Å³
包络体积 envelope_volume	361860 Å³
水化壳体积 shell_volume	74232 Å³
包络直径 envelope_diameter	118.3 Å
壳层 Rg shell_rg	47.95 Å
包络 Rg envelope_rg	37.32 Å
形状 Rg shape_rg	37.95 Å
总 Rg total_rg	38.54 Å
总原子数 total_atoms	16648
残基数 n_residues	2000
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	115.2 Å
Rg (实空间) rg_real	38.70 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	7.7010e+08
I(0) 误差 (实空间) i0_real_error	1.2320e+07
Rg (倒空间) rg_reciprocal	38.95 Å
I(0) (倒空间) i0_reciprocal	770300000.0000
解质量估计 total_estimate	0.8982
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	54.7 Å
偏度 Skewness skewness	-0.051
峰度 Kurtosis kurtosis	-0.619
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	233700000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.923

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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	Beta-xylosidase
分子量 formula_weight	58739.2 kDa
EC 编号 ec_number	3.2.1.37
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	17868

MIKVRVPDFSDKKFSDRWRYCVGTGRLGLALQKEYIETLKYVKENIDFKYIRGHGLLCDDVGIYREDVVGDEVKPFYNFTYIDRIFDSFLEIGIRPFVEIGFMPKKLASGTQTVFYWEGNVTPPKDYEKWSDLVKAVLHHFISRYGIEEVLKWPFEIWNEPNLKEFWKDADEKEYFKLYKVTAKAIKEVNENLKVGGPAICGGADYWIEDFLNFCYEENVPVDFVSRHAYTSKQGEYTPHLIYQEIMPSEYMLNEFKTVREIIKNSHFPNLPFHITEYNTSYSPQNPVHDTPFNAAYIARILSEGGDYVDSFSYWTFSDVFEERDVPRSQFHGGFGLVALNMIPKPTFYTFKFFNAMGEEMLYRDEHMLVTRRDDGSVALIAWNEVMDKTENPDEDYEVEIPVRFRDVFIKRQLIDEEHGNPWGTWIHMGRPRYPSKEQVNTLREVAKPEIMTSQPVANDGYLNLKFKLGKNAVVLYELTERIDESSTYIGLDDSKINGY

来源 Source

来源生物 organism	Thermoanaerobacterium saccharolyticum
NCBI 分类编号 ncbi_taxonomy_id	28896
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	1,5-anhydro-2-deoxy-2-fluoro-D-xylitol
分子量 formula_weight	136.1 kDa
来源方法 src_method	syn
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	1220

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1uhva1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

结构域编号 domain_id	d1uhva2
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	d1uhvb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

结构域编号 domain_id	d1uhvb2
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	d1uhvc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

结构域编号 domain_id	d1uhvc2
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	d1uhvd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

结构域编号 domain_id	d1uhvd2
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 (8 domains)

结构域编号 domain_id	1uhvA01
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	1500 — Glycosyl hydrolase domain; family 39

结构域编号 domain_id	1uhvA02
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	1uhvB01
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	1500 — Glycosyl hydrolase domain; family 39

结构域编号 domain_id	1uhvB02
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	1uhvC01
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	1500 — Glycosyl hydrolase domain; family 39

结构域编号 domain_id	1uhvC02
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	1uhvD01
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	1500 — Glycosyl hydrolase domain; family 39

结构域编号 domain_id	1uhvD02
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	95.326 Å
晶胞边长 b length_b	152.276 Å
晶胞边长 c length_c	159.684 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	16

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	32.330 Å
R 因子 r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2620

fit	/app/data/saxs_computation/uh/1uhv/1uhv.fit
pddf	/app/data/pr_computation/uh/1uhv/1uhv.pr.out
profile	/app/data/saxs_computation/uh/1uhv/1uhv.dat