SAXSdb — 1px8

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1px8
沉积日期 deposition_date	2003-07-03
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	34.19 Å
回转半径 Rg (电子) rg_electron	33.25 Å
零角强度 I(0) i0	202658000.00
分子量 molecular_weight	117600.0 kDa
排除体积 excluded_volume	148140 Å³
包络体积 envelope_volume	190000 Å³
水化壳体积 shell_volume	46645 Å³
包络直径 envelope_diameter	108.4 Å
壳层 Rg shell_rg	40.53 Å
包络 Rg envelope_rg	34.00 Å
形状 Rg shape_rg	33.21 Å
总 Rg total_rg	33.95 Å
总原子数 total_atoms	8328
残基数 n_residues	1000
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	109.3 Å
Rg (实空间) rg_real	34.17 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	2.0270e+08
I(0) 误差 (实空间) i0_real_error	3.5160e+06
Rg (倒空间) rg_reciprocal	34.19 Å
I(0) (倒空间) i0_reciprocal	202700000.0000
解质量估计 total_estimate	0.9030
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	35.6 Å
偏度 Skewness skewness	0.276
峰度 Kurtosis kurtosis	-0.619
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	72210000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.954

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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	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	8655

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	beta-D-xylopyranose
分子量 formula_weight	150.1 kDa
来源方法 src_method	man
拷贝数 entity_count	2

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	327

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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	d1px8a1
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	d1px8a2
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	d1px8b1
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	d1px8b2
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	1px8A01
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	1px8A02
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	1px8B01
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	1px8B02
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	92.719 Å
晶胞边长 b length_b	92.719 Å
晶胞边长 c length_c	241.296 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 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	19.910 Å
R 因子 r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2710

fit	/app/data/saxs_computation/px/1px8/1px8.fit
pddf	/app/data/pr_computation/px/1px8/1px8.pr.out
profile	/app/data/saxs_computation/px/1px8/1px8.dat

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

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