SAXSdb — 1ogs

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ogs
沉积日期 deposition_date	2003-05-13
结构标题 title	human acid-beta-glucosidase
关键词 keywords	;HYDROLASE, GAUCHER DISEASE, GLUCOSIDASE, GLUCOCEREBROSIDASE, CEREZYME HYDROLASE, GLYCOSIDASE, SPHINGOLIPID METABOLISM, GLYCOPROTE LYSOSOME, MEMBRANE, DISEASE MUTATI POLYMORPHISM, ALTERNATIVE INITIATION, PHARMACEUTICAL, ISRAEL STRUCTURAL PROTEOMICS CENTER, ISPC, STRUCTURAL GENOMICS ;; 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	39.44 Å
回转半径 Rg (电子) rg_electron	39.78 Å
零角强度 I(0) i0	191843000.00
分子量 molecular_weight	113190.0 kDa
排除体积 excluded_volume	141560 Å³
包络体积 envelope_volume	172440 Å³
水化壳体积 shell_volume	38293 Å³
包络直径 envelope_diameter	140.1 Å
壳层 Rg shell_rg	42.01 Å
包络 Rg envelope_rg	39.77 Å
形状 Rg shape_rg	39.76 Å
总 Rg total_rg	39.97 Å
总原子数 total_atoms	7976
残基数 n_residues	994
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	138.6 Å
Rg (实空间) rg_real	40.05 Å
Rg 误差 (实空间) rg_real_error	1.62 Å
I(0) (实空间) i0_real	1.9180e+08
I(0) 误差 (实空间) i0_real_error	3.7800e+06
Rg (倒空间) rg_reciprocal	39.68 Å
I(0) (倒空间) i0_reciprocal	191800000.0000
解质量估计 total_estimate	0.7425
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	31.2 Å
偏度 Skewness skewness	0.519
峰度 Kurtosis kurtosis	-0.604
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	42550000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.471; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.411; Smooth: 0.822

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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 (5)

Entity 1 polymer

描述 description	Glucosylceramidase
分子量 formula_weight	55640.2 kDa
EC 编号 ec_number	3.2.1.45,2.4.1.-,3.2.1.104
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	9020

ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

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	1

Entity 3 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	15

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	1

Entity 5 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	938

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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	d1ogsa1
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.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

结构域编号 domain_id	d1ogsa2
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.1.8.3 — beta-glycanases

结构域编号 domain_id	d1ogsb1
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.71.1.2 — Composite domain of glycosyl hydrolase families 5, 30, 39 and 51

结构域编号 domain_id	d1ogsb2
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.1.8.3 — beta-glycanases

CATH v4.4 (4 domains)

结构域编号 domain_id	1ogsA01
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	1ogsA02
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	1ogsB01
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	1ogsB02
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	107.735 Å
晶胞边长 b length_b	285.232 Å
晶胞边长 c length_c	91.678 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	16

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	2.000 Å
最低分辨率 resolution_low	14.400 Å
R 因子 r_factor	0.1950
R_work r_work	0.1950
R_free r_free	0.2300

fit	/app/data/saxs_computation/og/1ogs/1ogs.fit
pddf	/app/data/pr_computation/og/1ogs/1ogs.pr.out
profile	/app/data/saxs_computation/og/1ogs/1ogs.dat

human acid-beta-glucosidase

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

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

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction