SAXSdb — 1y9m

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1y9m
沉积日期 deposition_date	2004-12-16
结构标题 title	Crystal structure of exo-inulinase from Aspergillus awamori in spacegroup P212121
关键词 keywords	Exo-inulinase, Aspergillus awamori, Glycoside hydrolase family 32, Crystallographic structure, native structure, 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	24.34 Å
回转半径 Rg (电子) rg_electron	23.29 Å
零角强度 I(0) i0	58674800.00
分子量 molecular_weight	59443.0 kDa
排除体积 excluded_volume	73979 Å³
包络体积 envelope_volume	85036 Å³
水化壳体积 shell_volume	29677 Å³
包络直径 envelope_diameter	83.1 Å
壳层 Rg shell_rg	31.35 Å
包络 Rg envelope_rg	23.80 Å
形状 Rg shape_rg	23.23 Å
总 Rg total_rg	24.33 Å
总原子数 total_atoms	4208
残基数 n_residues	517
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	80.8 Å
Rg (实空间) rg_real	24.28 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	5.8670e+07
I(0) 误差 (实空间) i0_real_error	7.9490e+05
Rg (倒空间) rg_reciprocal	24.29 Å
I(0) (倒空间) i0_reciprocal	58680000.0000
解质量估计 total_estimate	0.8762
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	28.2 Å
偏度 Skewness skewness	0.344
峰度 Kurtosis kurtosis	-0.232
角度范围 angular_range	— – 0.3250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	15290000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.975

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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 (7)

Entity 1 polymer

描述 description	exo-inulinase
分子量 formula_weight	57188.6 kDa
EC 编号 ec_number	3.2.1.80
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4847

FNYDQPYRGQYHFSPQKNWMNDPNGLLYHNGTYHLFFQYNPGGIEWGNISWGHAISEDLTHWEEKPVALLARGFGSDVTEMYFSGSAVADVNNTSGFGKDGKTPLVAMYTSYYPVAQTLPSGQTVQEDQQSQSIAYSLDDGLTWTTYDAANPVIPNPPSPYEAEYQNFRDPFVFWHDESQKWVVVTSIAELHKLAIYTSDNLKDWKLVSEFGPYNAQGGVWECPGLVKLPLDSGNSTKWVITSGLNPGGPPGTVGSGTQYFVGEFDGTTFTPDADTVYPGNSTANWMDWGPDFYAAAGYNGLSLNDHVHIGWMNNWQYGANIPTYPWRSAMAIPRHMALKTIGSKATLVQQPQEAWSSISNKRPIYSRTFKTLSEGSTNTTTTGETFKVDLSFSAKSKASTFAIALRASANFTEQTLVGYDFAKQQIFLDRTHSGDVSFDETFASVYHGPLTPDSTGVVKLSIFVDRSSVEVFGGQGETTLTAQIFPSSDAVHARLASTGGTTEDVRADIYKIASTWN

Entity 2 branched

描述 description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	alpha-D-mannopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 6 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 7 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	639

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1y9ma1
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.29.1.19 — Glycosyl hydrolases family 32 C-terminal domain

结构域编号 domain_id	d1y9ma2
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.67.2.3 — Glycosyl hydrolases family 32 N-terminal domain

CATH v4.4 (2 domains)

结构域编号 domain_id	1y9mA01
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	1y9mA02
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	560 — Exo-inulinase; domain 1

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7. 引用文献 (2)

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晶胞边长 a length_a	64.816 Å
晶胞边长 b length_b	82.131 Å
晶胞边长 c length_c	136.219 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	4

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	1.890 Å
最低分辨率 resolution_low	19.900 Å
R 因子 r_factor	0.1666
R_work r_work	0.1649
R_free r_free	0.1997

fit	/app/data/saxs_computation/y9/1y9m/1y9m.fit
pddf	/app/data/pr_computation/y9/1y9m/1y9m.pr.out
profile	/app/data/saxs_computation/y9/1y9m/1y9m.dat

Crystal structure of exo-inulinase from Aspergillus awamori in spacegroup P212121

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution