SAXSdb — 1mxd

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1mxd
沉积日期 deposition_date	2002-10-02
结构标题 title	Structure of a (Ca,Zn)-dependent alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei
关键词 keywords	(beta/alpha)8-barrel, alpha-amylase, family 13 glycosyl hydrolase, 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	24.33 Å
回转半径 Rg (电子) rg_electron	23.46 Å
零角强度 I(0) i0	43984300.00
分子量 molecular_weight	52619.0 kDa
排除体积 excluded_volume	65789 Å³
包络体积 envelope_volume	71240 Å³
水化壳体积 shell_volume	25911 Å³
包络直径 envelope_diameter	88.1 Å
壳层 Rg shell_rg	30.33 Å
包络 Rg envelope_rg	23.74 Å
形状 Rg shape_rg	23.47 Å
总 Rg total_rg	24.19 Å
总原子数 total_atoms	3718
残基数 n_residues	435
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	84.4 Å
Rg (实空间) rg_real	24.40 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	4.3980e+07
I(0) 误差 (实空间) i0_real_error	7.3890e+05
Rg (倒空间) rg_reciprocal	24.39 Å
I(0) (倒空间) i0_reciprocal	43980000.0000
解质量估计 total_estimate	0.8552
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	26.8 Å
偏度 Skewness skewness	0.476
峰度 Kurtosis kurtosis	-0.150
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	7506000.0000
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: 0.737; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.987

▶

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

▶

5. 实体与聚合体信息 (7)

Entity 1 polymer

描述 description	alpha amylase
分子量 formula_weight	50228.7 kDa
EC 编号 ec_number	3.2.1.1
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	4007

AKYLELEEGGVIMQAFYWDVPGGGIWWDHIRSKIPEWYEAGISAIWLPPPSKGMSGGYSMGYDPYDYFDLGEYYQKGTVETRFGSKEELVRLIQTAHAYGIKVIADVVINHRAGGDLEWNPFVGDYTWTDFSKVASGKYTANYLDFHPNELHCCDEGTFGGFPDICHHKEWDQYWLWKSNESYAAYLRSIGFDGWRFDYVKGYGAWVVRDWLNWWGGWAVGEYWDTNVDALLSWAYESGAKVFDFPLYYKMDEAFDNNNIPALVYALQNGQTVVSRDPFKAVTFVANHDTDIIWNKYPAYAFILTYEGQPVIFYRDFEEWLNKDKLINLIWIHDHLAGGSTTIVYYDNDELIFVRNGDSRRPGLITYINLSPNWVGRWVYVPKFAGACIHEYTGNLGGWVDKRVDSSGWVYLEAPPHDPANGYYGYSVWSYCGVG

来源 Source

来源生物 organism	Pyrococcus woesei
NCBI 分类编号 ncbi_taxonomy_id	2262
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

描述 description	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	645.6 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 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	6

Entity 4 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	1

Entity 5 non-polymer

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

Entity 6 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	289

▼

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1mxda1
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.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

结构域编号 domain_id	d1mxda2
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.1.8.1 — Amylase, catalytic domain

CATH v4.4 (2 domains)

结构域编号 domain_id	1mxdA01
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	1mxdA02
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	1180 — Golgi alpha-mannosidase II

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	62.837 Å
晶胞边长 b length_b	77.207 Å
晶胞边长 c length_c	106.569 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	2.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1900
R_work r_work	0.1900
R_free r_free	0.2150

fit	/app/data/saxs_computation/mx/1mxd/1mxd.fit
pddf	/app/data/pr_computation/mx/1mxd/1mxd.pr.out
profile	/app/data/saxs_computation/mx/1mxd/1mxd.dat

Structure of a (Ca,Zn)-dependent alpha-amylase from the hyperthermophilic archaeon Pyrococcus woesei

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution