SAXSdb — 2gvy

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2gvy
沉积日期 deposition_date	2006-05-03
结构标题 title	Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 A resolution
关键词 keywords	(BETA-ALPHA)8 BARREL, 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	31.33 Å
回转半径 Rg (电子) rg_electron	30.30 Å
零角强度 I(0) i0	183856000.00
分子量 molecular_weight	107100.0 kDa
排除体积 excluded_volume	133090 Å³
包络体积 envelope_volume	153410 Å³
水化壳体积 shell_volume	41235 Å³
包络直径 envelope_diameter	97.9 Å
壳层 Rg shell_rg	38.26 Å
包络 Rg envelope_rg	30.28 Å
形状 Rg shape_rg	30.31 Å
总 Rg total_rg	30.92 Å
总原子数 total_atoms	7540
残基数 n_residues	952
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	98.2 Å
Rg (实空间) rg_real	31.23 Å
Rg 误差 (实空间) rg_real_error	0.45 Å
I(0) (实空间) i0_real	1.8390e+08
I(0) 误差 (实空间) i0_real_error	2.6400e+06
Rg (倒空间) rg_reciprocal	31.28 Å
I(0) (倒空间) i0_reciprocal	183900000.0000
解质量估计 total_estimate	0.9090
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	34.7 Å
偏度 Skewness skewness	0.204
峰度 Kurtosis kurtosis	-0.611
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	53280000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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 (6)

Entity 1 polymer

描述 description	Alpha-amylase A
分子量 formula_weight	52526.0 kDa
EC 编号 ec_number	3.2.1.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	8293

ATPADWRSQSIYFLLTDRFARTDGSTTATCNTADQKYCGGTWQGIIDKLDYIQGMGFTAIWITPVTAQLPQTTAYGDAYHGYWQQDIYSLNENYGTADDLKALSSALHERGMYLMVDVVANHMGYDGAGSSVDYSVFKPFSSQDYFHPFCFIQNYEDQTQVEDCWLGDNTVSLPDLDTTKDVVKNEWYDWVGSLVSNYSIDGLRIDTVKHVQKDFWPGYNKAAGVYCIGEVLDGDPAYTCPYQNVMDGVLNYPIYYPLLNAFKSTSGSMDDLYNMINTVKSDCPDSTLLGTFVENHDNPRFASYTNDIALAKNVAAFIILNDGIPIIYAGQEQHYAGGNDPANREATWLSGYPTDSELYKLIASANAIRNYAISKDTGFVTYKNWPIYKDDTTIAMRKGTDGSQIVTILSNKGASGDSYTLSLSGAGYTAGQQLTEVIGCTTVTVGSDGNVPVPMAGGLPRVLYPTEKLAGSKICSSS

来源 Source

来源生物 organism	Aspergillus oryzae
NCBI 分类编号 ncbi_taxonomy_id	5062
宿主生物 host_organism	Aspergillus oryzae

Entity 2 branched

描述 description	alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 3 branched

描述 description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 4 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	2

Entity 5 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	2

Entity 6 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	751

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2gvya1
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	d2gvya2
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

结构域编号 domain_id	d2gvyb1
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	d2gvyb2
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 (4 domains)

结构域编号 domain_id	2gvyA01
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	2gvyA02
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

结构域编号 domain_id	2gvyB01
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	2gvyB02
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

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7. 引用文献 (1)

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晶胞边长 a length_a	65.451 Å
晶胞边长 b length_b	101.149 Å
晶胞边长 c length_c	75.185 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.89 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1650
R_work r_work	0.1620
R_free r_free	0.2100

fit	/app/data/saxs_computation/gv/2gvy/2gvy.fit
pddf	/app/data/pr_computation/gv/2gvy/2gvy.pr.out
profile	/app/data/saxs_computation/gv/2gvy/2gvy.dat

Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 A resolution

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution