2exh

Structure of the family43 beta-Xylosidase from geobacillus stearothermophilus

Method: X-RAY DIFFRACTION D_max: 121.9 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	2exh
沉积日期 deposition_date	2005-11-08
结构标题 title	Structure of the family43 beta-Xylosidase from geobacillus stearothermophilus
关键词 keywords	glykosidase, hydrolsase, xylosidase, family43, 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	39.30 Å
回转半径 Rg (电子) rg_electron	38.45 Å
零角强度 I(0) i0	890910000.00
分子量 molecular_weight	247750.0 kDa
排除体积 excluded_volume	310070 Å³
包络体积 envelope_volume	378390 Å³
水化壳体积 shell_volume	77450 Å³
包络直径 envelope_diameter	120.0 Å
壳层 Rg shell_rg	47.83 Å
包络 Rg envelope_rg	37.80 Å
形状 Rg shape_rg	38.44 Å
总 Rg total_rg	38.96 Å
总原子数 total_atoms	17568
残基数 n_residues	2132
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	121.9 Å
Rg (实空间) rg_real	38.95 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	8.9090e+08
I(0) 误差 (实空间) i0_real_error	1.4900e+07
Rg (倒空间) rg_reciprocal	39.17 Å
I(0) (倒空间) i0_reciprocal	891100000.0000
解质量估计 total_estimate	0.8911
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	54.8 Å
偏度 Skewness skewness	0.044
峰度 Kurtosis kurtosis	-0.526
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	856200000.0000
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: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.949

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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	beta-D-xylosidase
分子量 formula_weight	61985.3 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	19399

MSKIKNPILTGFHPDPSICRVGDDYYIAVSTFEWFPGVRIYHSKDLKNWRLVARPLNRLSQLNMIGNPDSGGVWAPHLSYSDGKFWLIYTDVKVVEGQWKDGHNYLVTCDTIDGAWSDPIYLNSSGFDPSLFHDEDGRKYLVNMYWDHRVDHHPFYGIVLQEYSVEQKKLVGEPKIIFKGTDLRITEGPHLYKINGYYYLLTAEGGTRYNHAATIARSTSLYGPYEVHPDNPLLTSWPYPRNPLQKAGHASIVHTHTDEWFLVHLTGRPLPREGQPLLEHRGYCPLGRETAIQRLEWKDGWPYVVGGNGPSLEIDGPSVEEVSWEKDYDEKDDFDGDTLNHHFQTLRIPLGEDIATLKARPGHLRLYGRESLTSRFTQAFVARRWQHFHFVAETKVSFRPTTFQQSAGLVNYYNTQNWTTLQITWHEEKGRILELMTCDHLVVDQPLRGREIVVPDDIEYVYLRVTVQATTYKYSYSFDGMNWIDLPVTFESYKLSDDYIKSRAAFTGAFVGMHCRDGSGQNNYADFDYFLYKEL

来源 Source

来源生物 organism	Geobacillus stearothermophilus
NCBI 分类编号 ncbi_taxonomy_id	1422
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	4

Entity 3 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	3

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 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	1831

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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	d2exha1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.23 — Beta-D-xylosidase C-terminal domain-like

结构域编号 domain_id	d2exha2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.67 — 5-bladed beta-propeller
超家族 Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
家族 Family family	b.67.2.1 — alpha-L-arabinanase-like

结构域编号 domain_id	d2exhb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.23 — Beta-D-xylosidase C-terminal domain-like

结构域编号 domain_id	d2exhb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.67 — 5-bladed beta-propeller
超家族 Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
家族 Family family	b.67.2.1 — alpha-L-arabinanase-like

结构域编号 domain_id	d2exhc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.23 — Beta-D-xylosidase C-terminal domain-like

结构域编号 domain_id	d2exhc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.67 — 5-bladed beta-propeller
超家族 Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
家族 Family family	b.67.2.1 — alpha-L-arabinanase-like

结构域编号 domain_id	d2exhd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.29 — Concanavalin A-like lectins/glucanases
超家族 Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
家族 Family family	b.29.1.23 — Beta-D-xylosidase C-terminal domain-like

结构域编号 domain_id	d2exhd2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.67 — 5-bladed beta-propeller
超家族 Superfamily superfamily	b.67.2 — Arabinanase/levansucrase/invertase
家族 Family family	b.67.2.1 — alpha-L-arabinanase-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2exhA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	115 — 5 Propeller
拓扑 Topology topology	10 — Tachylectin-2; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

结构域编号 domain_id	2exhA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	2exhB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	115 — 5 Propeller
拓扑 Topology topology	10 — Tachylectin-2; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

结构域编号 domain_id	2exhB02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	2exhC01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	115 — 5 Propeller
拓扑 Topology topology	10 — Tachylectin-2; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

结构域编号 domain_id	2exhC02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

结构域编号 domain_id	2exhD01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	115 — 5 Propeller
拓扑 Topology topology	10 — Tachylectin-2; Chain A
同源超家族 H-superfamily homologous superfamily	20 — Glycosyl hydrolase domain; family 43

结构域编号 domain_id	2exhD02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	200 —

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7. 引用文献 (3)

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晶胞边长 a length_a	140.027 Å
晶胞边长 b length_b	140.027 Å
晶胞边长 c length_c	231.599 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	32

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	1.880 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.2350
R_work r_work	0.2330
R_free r_free	0.2860

fit	/app/data/saxs_computation/ex/2exh/2exh.fit
pddf	/app/data/pr_computation/ex/2exh/2exh.pr.out
profile	/app/data/saxs_computation/ex/2exh/2exh.dat