2aey

Crystal structure of fructan 1-exohydrolase IIa from Cichorium intybus in complex with 2,5 dideoxy-2,5-immino-D-mannitol

Method: X-RAY DIFFRACTION D_max: 77.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2aey
沉积日期 deposition_date	2005-07-25
结构标题 title	Crystal structure of fructan 1-exohydrolase IIa from Cichorium intybus in complex with 2,5 dideoxy-2,5-immino-D-mannitol
关键词 keywords	five fold beta propeller, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	24.57 Å
回转半径 Rg (电子) rg_electron	23.54 Å
零角强度 I(0) i0	63473600.00
分子量 molecular_weight	61583.0 kDa
排除体积 excluded_volume	76646 Å³
包络体积 envelope_volume	89185 Å³
水化壳体积 shell_volume	30517 Å³
包络直径 envelope_diameter	79.1 Å
壳层 Rg shell_rg	31.71 Å
包络 Rg envelope_rg	23.91 Å
形状 Rg shape_rg	23.50 Å
总 Rg total_rg	24.57 Å
总原子数 total_atoms	4352
残基数 n_residues	537
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	77.7 Å
Rg (实空间) rg_real	24.47 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	6.3470e+07
I(0) 误差 (实空间) i0_real_error	8.8930e+05
Rg (倒空间) rg_reciprocal	24.50 Å
I(0) (倒空间) i0_reciprocal	63470000.0000
解质量估计 total_estimate	0.8997
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	28.4 Å
偏度 Skewness skewness	0.259
峰度 Kurtosis kurtosis	-0.407
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	17870000.0000
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: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	fructan 1-exohydrolase IIa
分子量 formula_weight	61116.0 kDa
EC 编号 ec_number	3.2.1.153
来源方法 src_method	man
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	4362

QQIEQPYRTGYHFQPPSNWMNDPNGPMLYQGVYHFFYQYNPYAATFGDVIIWGHAVSYDLVNWIHLDPAIYPTQEADSKSCWSGSATILPGNIPAMLYTGSDSKSRQVQDLAWPKNLSDPFLREWVKHPKNPLITPPEGVKDDCFRDPSTAWLGPDGVWRIVVGGDRDNNGMAFLYQSTDFVNWKRYDQPLSSADATGTWECPDFYPVPLNSTNGLDTSVYGGSVRHVMKAGFEGHDWYTIGTYSPDRENFLPQNGLSLTGSTLDLRYDYGQFYASKSFFDDAKNRRVLWAWVPETDSQADDIEKGWAGLQSFPRALWIDRNGKQLIQWPVEEIEELRQNQVNLQNKNLKPGSVLEIHGIAASQADVTISFKLEGLKEAEVLDTTLVDPQALCNERGASSRGALGPFGLLAMASKDLKEQSAIFFRVFQNQLGRYSVLMCSDLSRSTVRSNIDTTSYGAFVDIDPRSEEISLRNLIDHSIIESFGAGGKTCITSRIYPKFVNNEEAHLFVFNNGTQNVKISEMSAWSMKNAKFVVDQSVKSAA

来源 Source

来源生物 organism	Cichorium intybus
通用名 common_name	chicory
NCBI 分类编号 ncbi_taxonomy_id	13427
宿主生物 host_organism	Pichia pastoris

Entity 2 branched

描述 description	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	586.5 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	2,5-DIDEOXY-2,5-IMINO-D-MANNITOL
分子量 formula_weight	163.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	10

▼

6. 折叠分类 (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

结构域编号 domain_id	2aeyA01
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	2aeyA02
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	138.860 Å
晶胞边长 b length_b	138.860 Å
晶胞边长 c length_c	182.440 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 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	3.270 Å
最低分辨率 resolution_low	29.700 Å
R 因子 r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2570

fit	/app/data/saxs_computation/ae/2aey/2aey.fit
pddf	/app/data/pr_computation/ae/2aey/2aey.pr.out
profile	/app/data/saxs_computation/ae/2aey/2aey.dat