1up6
;Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom resolution in the tetragonal form with manganese, NAD+ and glucose-6-phosphate ;
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
| 条目编号 entry_id | 1up6 |
| 沉积日期 deposition_date | 2003-09-29 |
| 结构标题 title | ;Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom resolution in the tetragonal form with manganese, NAD+ and glucose-6-phosphate ; |
| 关键词 keywords | HYDROLASE, 6-PHOSPHO-BETA-GLUCOSIDASE, FAMILY4 HYDROLASE, NAD DEPENDENT; HYDROLASE |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 57.80 Å |
| 回转半径 Rg (电子) rg_electron | 58.05 Å |
| 零角强度 I(0) i0 | 1892450000.00 |
| 分子量 molecular_weight | 375930.0 kDa |
| 排除体积 excluded_volume | 473900 ų |
| 包络体积 envelope_volume | 647080 ų |
| 水化壳体积 shell_volume | 94429 ų |
| 包络直径 envelope_diameter | 198.2 Å |
| 壳层 Rg shell_rg | 58.03 Å |
| 包络 Rg envelope_rg | 57.01 Å |
| 形状 Rg shape_rg | 58.01 Å |
| 总 Rg total_rg | 58.20 Å |
| 总原子数 total_atoms | 26344 |
| 残基数 n_residues | 3169 |
| 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/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 181.1 Å |
| Rg (实空间) rg_real | 58.16 Å |
| Rg 误差 (实空间) rg_real_error | 1.66 Å |
| I(0) (实空间) i0_real | 1.8920e+09 |
| I(0) 误差 (实空间) i0_real_error | 4.0370e+07 |
| Rg (倒空间) rg_reciprocal | 57.46 Å |
| I(0) (倒空间) i0_reciprocal | 1890000000.0000 |
| 解质量估计 total_estimate | 0.8195 |
| 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 | 60.4 Å |
| 偏度 Skewness skewness | 0.459 |
| 峰度 Kurtosis kurtosis | -0.513 |
| 角度范围 angular_range | — – 0.1350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 111300000.0000 |
| 实空间数据点数 n_real_points | 28 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.014 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 32 domains
SCOP 2.08 (16 domains)
| 结构域编号 domain_id | d1up6a1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d1up6a2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.2 — AglA-like glucosidase |
| 结构域编号 domain_id | d1up6b1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d1up6b2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.2 — AglA-like glucosidase |
| 结构域编号 domain_id | d1up6c1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d1up6c2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.2 — AglA-like glucosidase |
| 结构域编号 domain_id | d1up6d1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d1up6d2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.2 — AglA-like glucosidase |
| 结构域编号 domain_id | d1up6e1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d1up6e2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.2 — AglA-like glucosidase |
| 结构域编号 domain_id | d1up6f1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d1up6f2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.2 — AglA-like glucosidase |
| 结构域编号 domain_id | d1up6g1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d1up6g2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.2 — AglA-like glucosidase |
| 结构域编号 domain_id | d1up6h1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d1up6h2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.2 — AglA-like glucosidase |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 1up6A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1up6A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |
| 结构域编号 domain_id | 1up6B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1up6B02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |
| 结构域编号 domain_id | 1up6C01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1up6C02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |
| 结构域编号 domain_id | 1up6D01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1up6D02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |
| 结构域编号 domain_id | 1up6E01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1up6E02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |
| 结构域编号 domain_id | 1up6F01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1up6F02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |
| 结构域编号 domain_id | 1up6G01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1up6G02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |
| 结构域编号 domain_id | 1up6H01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1up6H02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |