1myr

MYROSINASE FROM SINAPIS ALBA

Method: X-RAY DIFFRACTION D_max: 74.8 Å Quality: REASONABLE

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	1myr
沉积日期 deposition_date	1997-03-23
结构标题 title	MYROSINASE FROM SINAPIS ALBA
关键词 keywords	FAMILY 1 GLYCOSYL HYDROLASE, GLUCOSINOLATE, MYROSINASE, TIM BARREL, GLYCOSIDASE; GLYCOSIDASE
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	23.73 Å
回转半径 Rg (电子) rg_electron	22.27 Å
零角强度 I(0) i0	65571800.00
分子量 molecular_weight	61836.0 kDa
排除体积 excluded_volume	76426 Å³
包络体积 envelope_volume	86659 Å³
水化壳体积 shell_volume	30727 Å³
包络直径 envelope_diameter	78.4 Å
壳层 Rg shell_rg	30.70 Å
包络 Rg envelope_rg	22.82 Å
形状 Rg shape_rg	22.18 Å
总 Rg total_rg	23.40 Å
总原子数 total_atoms	4342
残基数 n_residues	499
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	74.8 Å
Rg (实空间) rg_real	23.74 Å
Rg 误差 (实空间) rg_real_error	0.13 Å
I(0) (实空间) i0_real	6.3870e+07
I(0) 误差 (实空间) i0_real_error	7.0220e+05
Rg (倒空间) rg_reciprocal	23.59 Å
I(0) (倒空间) i0_reciprocal	65570000.0000
解质量估计 total_estimate	0.7009
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	30.4 Å
偏度 Skewness skewness	0.191
峰度 Kurtosis kurtosis	-0.247
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	6.6660
最高正则化参数 α highest_alpha	14080000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.872; Stabil: 0.930; Sysdev: 0.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.745

▶

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

▶

5. 实体与聚合体信息 (9)

Entity 1 polymer

描述 description	MYROSINASE
分子量 formula_weight	56886.1 kDa
EC 编号 ec_number	3.2.3.1
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	5014

DEEITCQENNPFTCGNTDGLNSSSFEADFIFGVASSAYQIEGTIGRGLNIWDGFTHRYPDKSGPDHGNGDTTCDSFSYWQKDIDVLDELNATGYRFSIAWSRIIPRGKRSRGVNQKGIDYYHGLIDGLIKKGITPFVTLFHWDLPQTLQDEYEGFLDPQIIDDFKDYADLCFEEFGDSVKYWLTINQLYSVPTRGYGSALDAPGRCSPTVDPSCYAGNSSTEPYIVAHHQLLAHAKVVDLYRKNYTHQGGKIGPTMITRWFLPYNDTDRHSIAATERMKQFFLGWFMGPLTNGTYPQIMIDTVGARLPTFSPEETNLVKGSYDFLGLNYYFTQYAQPSPNPVNATNHTAMMDAGAKLTYINASGHYIGPLFESDGGDGSSNIYYYPKGIYSVMDYFKNKYYNPLIYVTENGISTPGSENRKESMLDYTRIDYLCSHLCFLNKVIKEKDVNVKGYLAWALGDNYEFNNGFTVRFGLSYINWNNVTDRDLKKSGQWYQKFISP

Entity 2 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	2

Entity 3 branched

描述 description	;beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	864.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1189.1 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	5

Entity 6 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 8 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 9 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	672

▼

6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1myra_
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.1.8.4 — Family 1 of glycosyl hydrolase

CATH v4.4 (1 domains)

结构域编号 domain_id	1myrA00
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

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	134.300 Å
晶胞边长 b length_b	136.400 Å
晶胞边长 c length_c	80.300 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	1.640 Å
最低分辨率 resolution_low	17.400 Å
R 因子 r_factor	0.1520
R_work r_work	0.1520
R_free r_free	0.1870

fit	/app/data/saxs_computation/my/1myr/1myr.fit
pddf	/app/data/pr_computation/my/1myr/1myr.pr.out
profile	/app/data/saxs_computation/my/1myr/1myr.dat