SAXSdb — 1wpc

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wpc
沉积日期 deposition_date	2004-09-01
结构标题 title	Crystal structure of maltohexaose-producing amylase complexed with pseudo-maltononaose
关键词 keywords	Maltohexaose-producing amylase, alpha-amylase, acarbose, 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	25.03 Å
回转半径 Rg (电子) rg_electron	23.97 Å
零角强度 I(0) i0	56589900.00
分子量 molecular_weight	57197.0 kDa
排除体积 excluded_volume	70619 Å³
包络体积 envelope_volume	78147 Å³
水化壳体积 shell_volume	27600 Å³
包络直径 envelope_diameter	87.3 Å
壳层 Rg shell_rg	31.19 Å
包络 Rg envelope_rg	24.25 Å
形状 Rg shape_rg	23.96 Å
总 Rg total_rg	24.75 Å
总原子数 total_atoms	4041
残基数 n_residues	481
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	84.2 Å
Rg (实空间) rg_real	25.07 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	5.6590e+07
I(0) 误差 (实空间) i0_real_error	8.6050e+05
Rg (倒空间) rg_reciprocal	25.06 Å
I(0) (倒空间) i0_reciprocal	56590000.0000
解质量估计 total_estimate	0.8729
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	29.4 Å
偏度 Skewness skewness	0.457
峰度 Kurtosis kurtosis	-0.124
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10460000.0000
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: 0.800; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.991

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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 (8)

Entity 1 polymer

描述 description	Glucan 1,4-alpha-maltohexaosidase
分子量 formula_weight	55438.9 kDa
EC 编号 ec_number	3.2.1.98
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	4365

HHNGTNGTMMQYFEWYLPNDGNHWNRLNSDASNLKSKGITAVWIPPAWKGASQNDVGYGAYDLYDLGEFNQKGTVRTKYGTRSQLQAAVTSLKNNGIQVYGDVVMNHKGGADATEMVRAVEVNPNNRNQEVTGEYTIEAWTRFDFPGRGNTHSSFKWRWYHFDGVDWDQSRRLNNRIYKFRGHGKAWDWEVDTENGNYDYLMYADIDMDHPEVVNELRNWGVWYTNTLGLDGFRIDAVKHIKYSFTRDWINHVRSATGKNMFAVAEFWKNDLGAIENYLQKTNWNHSVFDVPLHYNLYNASKSGGNYDMRNIFNGTVVQRHPSHAVTFVDNHDSQPEEALESFVEEWFKPLAYALTLTREQGYPSVFYGDYYGIPTHGVPAMRSKIDPILEARQKYAYGKQNDYLDHHNIIGWTREGNTAHPNSGLATIMSDGAGGSKWMFVGRNKAGQVWSDITGNRTGTVTINADGWGNFSVNGGSVSIWVNK

来源 Source

来源生物 organism	Bacillus sp.
NCBI 分类编号 ncbi_taxonomy_id	1416
宿主生物 host_organism	Bacillus subtilis

Entity 2 branched

描述 description	4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	634.6 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-galactopyranose
分子量 formula_weight	472.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 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	2

Entity 5 non-polymer

描述 description	6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
分子量 formula_weight	175.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 6 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	3

Entity 7 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	324

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6. 折叠分类 (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1wpca1
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	d1wpca2
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 (3 domains)

结构域编号 domain_id	1wpcA01
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	1wpcA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	140 —

结构域编号 domain_id	1wpcA03
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 (2)

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晶胞边长 a length_a	47.410 Å
晶胞边长 b length_b	82.490 Å
晶胞边长 c length_c	126.880 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	1.900 Å
最低分辨率 resolution_low	6.000 Å
R 因子 r_factor	0.1720
R_work r_work	0.1720
R_free r_free	0.2070

fit	/app/data/saxs_computation/wp/1wpc/1wpc.fit
pddf	/app/data/pr_computation/wp/1wpc/1wpc.pr.out
profile	/app/data/saxs_computation/wp/1wpc/1wpc.dat

Crystal structure of maltohexaose-producing amylase complexed with pseudo-maltononaose

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution