SAXSdb — 1hxk

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hxk
沉积日期 deposition_date	2001-01-16
结构标题 title	GOLGI ALPHA-MANNOSIDASE II IN COMPLEX WITH DEOXYMANNOJIRIMICIN
关键词 keywords	N-terminal alpha-beta domain, three helix bundle, 2 C-terminal beta barrels, 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	30.48 Å
回转半径 Rg (电子) rg_electron	29.62 Å
零角强度 I(0) i0	213673000.00
分子量 molecular_weight	116510.0 kDa
排除体积 excluded_volume	145520 Å³
包络体积 envelope_volume	169510 Å³
水化壳体积 shell_volume	45967 Å³
包络直径 envelope_diameter	105.4 Å
壳层 Rg shell_rg	38.26 Å
包络 Rg envelope_rg	29.97 Å
形状 Rg shape_rg	29.62 Å
总 Rg total_rg	30.30 Å
总原子数 total_atoms	8215
残基数 n_residues	1014
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	101.2 Å
Rg (实空间) rg_real	30.41 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	2.1370e+08
I(0) 误差 (实空间) i0_real_error	3.1080e+06
Rg (倒空间) rg_reciprocal	30.44 Å
I(0) (倒空间) i0_reciprocal	213700000.0000
解质量估计 total_estimate	0.8763
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	37.0 Å
偏度 Skewness skewness	0.355
峰度 Kurtosis kurtosis	-0.190
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	85270000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.959

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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-MANNOSIDASE II
分子量 formula_weight	116222.8 kDa
EC 编号 ec_number	3.2.1.114
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	9198

CQDVVQDVPNVDVQMLELYDRMSFKDIDGGVWKQGWNIKYDPLKYNAHHKLKVFVVPHSHNDPGWIQTFEEYYQHDTKHILSNALRHLHDNPEMKFIWAEISYFARFYHDLGENKKLQMKSIVKNGQLEFVTGGWVMPDEANSHWRNVLLQLTEGQTWLKQFMNVTPTASWAIDPFGHSPTMPYILQKSGFKNMLIQRTHYSVKKELAQQRQLEFLWRQIWDNKGDTALFTHMMPFYSYDIPHTCGPDPKVCCQFDFKRMGSFGLSCPWKVPPRTISDQNVAARSDLLVDQWKKKAELYRTNVLLIPLGDDFRFKQNTEWDVQRVNYERLFEHINSQAHFNVQAQFGTLQEYFDAVHQAERAGQAEFPTLSGDFFTYADRSDNYWSGYYTSRPYHKRMDRVLMHYVRAAEMLSAWHSWDGMARIEERLEQARRELSLFQHHDGITGTAKTHVVVDYEQRMQEALKACQMVMQQSVYRLLTKPSIYSPDFSFSYFTLDDSRWPGSGVEDSRTTIILGEDILPSKHVVMHNTLPHWREQLVDFYVSSPFVSVTDLANNPVEAQVSPVWSWHHDTLTKTIHPQGSTTKYRIIFKARVPPMGLATYVLTISDSKPEHTSYASNLLLRKNPTSLPLGQYPEDVKFGDPREISLRVGNGPTLAFSEQGLLKSIQLTQDSPHVPVHFKFLKYGVRSHGDRSGAYLFLPNGPASPVELGQPVVLVTKGKLESSVSVGLPSVVHQTIMRGGAPEIRNLVDIGSLDNTEIVMRLETHIDSGDIFYTDLNGLQFIKRRRLDKLPLQANYYPIPSGMFIEDANTRLTLLTGQPLGGSSLASGELEIMQDRRLASDDERGLGQGVLDNKPVLHIYRLVLEKVNNCVRPSKLHPAGYLTSAAHKASQSLLDPLDKFIFAENEWIGAQGQFGGDHPSAREDLDVSVMRRLTKSSAKTQRVGYVLHRTNLMQCGTPEEHTQKLDVCHLLPNVARCERTTLTFLQNLEHLDGMVAPEVCPMETAAYVSSHSS

来源 Source

来源生物 organism	Drosophila melanogaster
通用名 common_name	fruit fly
NCBI 分类编号 ncbi_taxonomy_id	7227
宿主生物 host_organism	Drosophila melanogaster

Entity 2 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	1

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	1

Entity 4 non-polymer

描述 description	1-DEOXYMANNOJIRIMYCIN
分子量 formula_weight	163.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	(4R)-2-METHYLPENTANE-2,4-DIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	983

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1hxka1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
超家族 Superfamily superfamily	a.8.3 — Families 57/38 glycoside transferase middle domain
家族 Family family	a.8.3.1 — alpha-mannosidase, domain 2

结构域编号 domain_id	d1hxka2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.5 — Galactose mutarotase-like
家族 Family family	b.30.5.6 — alpha-mannosidase, C-terminal domain

结构域编号 domain_id	d1hxka3
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamily	c.6.2 — Glycoside hydrolase/deacetylase
家族 Family family	c.6.2.1 — alpha-mannosidase

CATH v4.4 (5 domains)

结构域编号 domain_id	1hxkA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	110 — 7-stranded beta/alpha barrel
同源超家族 H-superfamily homologous superfamily	10 — Glycoside hydrolase 38, N terminal domain

结构域编号 domain_id	1hxkA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily	50 — Glycoside hydrolase family 38, central domain

结构域编号 domain_id	1hxkA03
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	1hxkA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	30 — Golgi alpha-mannosidase II; domain 4

结构域编号 domain_id	1hxkA05
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	1360 —

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7. 引用文献 (1)

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晶胞边长 a length_a	68.814 Å
晶胞边长 b length_b	109.616 Å
晶胞边长 c length_c	138.281 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	1.500 Å
最低分辨率 resolution_low	85.900 Å
R 因子 r_factor	—
R_work r_work	0.1970
R_free r_free	0.2160

fit	/app/data/saxs_computation/hx/1hxk/1hxk.fit
pddf	/app/data/pr_computation/hx/1hxk/1hxk.pr.out
profile	/app/data/saxs_computation/hx/1hxk/1hxk.dat

GOLGI ALPHA-MANNOSIDASE II IN COMPLEX WITH DEOXYMANNOJIRIMICIN

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution