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1k08

;Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b ;

Method: X-RAY DIFFRACTION Dmax: 90.6 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

SAXS profile for 1k08

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1k08
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1. 结构基本信息 1. Structure Basics

条目编号 entry_id1k08
沉积日期 deposition_date2001-09-18
结构标题 title;Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b ;
关键词 keywordsglycogen phosphorylase, catalytic site, new allosteric site, TRANSFERASE; TRANSFERASE
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_guinier28.51 Å
回转半径 Rg (电子) rg_electron27.49 Å
零角强度 I(0) i0142062000.00
分子量 molecular_weight95053.0 kDa
排除体积 excluded_volume119250 ų
包络体积 envelope_volume140590 ų
水化壳体积 shell_volume40900 ų
包络直径 envelope_diameter95.7 Å
壳层 Rg shell_rg36.32 Å
包络 Rg envelope_rg27.83 Å
形状 Rg shape_rg27.50 Å
总 Rg total_rg28.28 Å
总原子数 total_atoms6704
残基数 n_residues817
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 dmax90.6 Å
Rg (实空间) rg_real28.34 Å
Rg 误差 (实空间) rg_real_error0.43 Å
I(0) (实空间) i0_real1.4210e+08
I(0) 误差 (实空间) i0_real_error1.8450e+06
Rg (倒空间) rg_reciprocal28.39 Å
I(0) (倒空间) i0_reciprocal142100000.0000
解质量估计 total_estimate0.8976
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary34.0 Å
偏度 Skewness skewness0.201
峰度 Kurtosis kurtosis-0.468
角度范围 angular_range— – 0.2800 Å−1
当前正则化参数 α current_alpha0.0001
最高正则化参数 α highest_alpha40440000.0000
实空间数据点数 n_real_points57
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; 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 (4)

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

结构域编号 domain_idd1k08a_
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.87 — UDP-Glycosyltransferase/glycogen phosphorylase
超家族 Superfamily superfamilyc.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
家族 Family familyc.87.1.4 — Oligosaccharide phosphorylase

CATH v4.4 (2 domains)

结构域编号 domain_id1k08A01
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily2000 — Glycogen Phosphorylase B;
结构域编号 domain_id1k08A02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily2000 — Glycogen Phosphorylase B;
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7. 引用文献 (2)

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8. 文件与曲线 (10)