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1r34

Golgi alpha-mannosidase II complex with 5-thio-D-mannopyranosylamidinium salt

Method: X-RAY DIFFRACTION Dmax: 101.3 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1r34

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1r34
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1r34
沉积日期 deposition_date2003-09-30
结构标题 titleGolgi alpha-mannosidase II complex with 5-thio-D-mannopyranosylamidinium salt
关键词 keywordsGlycosyl hydrolase family 38, HYDROLASE; HYDROLASE
实验方法 methodX-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_guinier30.51 Å
回转半径 Rg (电子) rg_electron29.65 Å
零角强度 I(0) i0214260000.00
分子量 molecular_weight116660.0 kDa
排除体积 excluded_volume145710 ų
包络体积 envelope_volume170120 ų
水化壳体积 shell_volume46070 ų
包络直径 envelope_diameter106.4 Å
壳层 Rg shell_rg38.25 Å
包络 Rg envelope_rg30.02 Å
形状 Rg shape_rg29.65 Å
总 Rg total_rg30.33 Å
总原子数 total_atoms8225
残基数 n_residues1014
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 Å−1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3
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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax101.3 Å
Rg (实空间) rg_real30.44 Å
Rg 误差 (实空间) rg_real_error0.65 Å
I(0) (实空间) i0_real2.1430e+08
I(0) 误差 (实空间) i0_real_error3.2050e+06
Rg (倒空间) rg_reciprocal30.47 Å
I(0) (倒空间) i0_reciprocal214300000.0000
解质量估计 total_estimate0.8725
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary37.0 Å
偏度 Skewness skewness0.358
峰度 Kurtosis kurtosis-0.183
角度范围 angular_range— – 0.2600 Å−1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha86810000.0000
实空间数据点数 n_real_points53
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.915
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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)

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

结构域编号 domain_idd1r34a1
类 Class classa — All alpha proteins
折叠类型 Fold folda.8 — immunoglobulin/albumin-binding domain-like
超家族 Superfamily superfamilya.8.3 — Families 57/38 glycoside transferase middle domain
家族 Family familya.8.3.1 — alpha-mannosidase, domain 2
结构域编号 domain_idd1r34a2
类 Class classb — All beta proteins
折叠类型 Fold foldb.30 — Supersandwich
超家族 Superfamily superfamilyb.30.5 — Galactose mutarotase-like
家族 Family familyb.30.5.6 — alpha-mannosidase, C-terminal domain
结构域编号 domain_idd1r34a3
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.6 — 7-stranded beta/alpha barrel
超家族 Superfamily superfamilyc.6.2 — Glycoside hydrolase/deacetylase
家族 Family familyc.6.2.1 — alpha-mannosidase

CATH v4.4 (5 domains)

结构域编号 domain_id1r34A01
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology110 — 7-stranded beta/alpha barrel
同源超家族 H-superfamily homologous superfamily10 — Glycoside hydrolase 38, N terminal domain
结构域编号 domain_id1r34A02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
同源超家族 H-superfamily homologous superfamily50 — Glycoside hydrolase family 38, central domain
结构域编号 domain_id1r34A03
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1180 — Golgi alpha-mannosidase II
结构域编号 domain_id1r34A04
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily30 — Golgi alpha-mannosidase II; domain 4
结构域编号 domain_id1r34A05
类 Class class2 — Mainly Beta
架构 Architecture architecture60 — Sandwich
拓扑 Topology topology40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily1360 —
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7. 引用文献 (1)

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8. 文件与曲线 (10)