1vkd
Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution
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 | 1vkd |
| 沉积日期 deposition_date | 2004-05-12 |
| 结构标题 title | Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution |
| 关键词 keywords | Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, hydrolase; 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 | 52.11 Å |
| 回转半径 Rg (电子) rg_electron | 52.06 Å |
| 零角强度 I(0) i0 | 702761000.00 |
| 分子量 molecular_weight | 225130.0 kDa |
| 排除体积 excluded_volume | 282020 ų |
| 包络体积 envelope_volume | 383020 ų |
| 水化壳体积 shell_volume | 64113 ų |
| 包络直径 envelope_diameter | 164.5 Å |
| 壳层 Rg shell_rg | 52.23 Å |
| 包络 Rg envelope_rg | 50.77 Å |
| 形状 Rg shape_rg | 52.10 Å |
| 总 Rg total_rg | 51.92 Å |
| 总原子数 total_atoms | 15869 |
| 残基数 n_residues | 1927 |
| 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 | 151.2 Å |
| Rg (实空间) rg_real | 52.18 Å |
| Rg 误差 (实空间) rg_real_error | 1.19 Å |
| I(0) (实空间) i0_real | 7.0280e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.3820e+07 |
| Rg (倒空间) rg_reciprocal | 52.03 Å |
| I(0) (倒空间) i0_reciprocal | 702600000.0000 |
| 解质量估计 total_estimate | 0.8216 |
| 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 | 60.5 Å |
| 偏度 Skewness skewness | 0.177 |
| 峰度 Kurtosis kurtosis | -0.927 |
| 角度范围 angular_range | — – 0.1500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 23250000.0000 |
| 实空间数据点数 n_real_points | 31 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.818; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 13 domains
SCOP 2.08 (7 domains)
| 结构域编号 domain_id | d1vkda1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.4 — TM1225-like predicted glycosylases |
| 结构域编号 domain_id | d1vkda2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1vkdb_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.4 — TM1225-like predicted glycosylases |
| 结构域编号 domain_id | d1vkdc_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.4 — TM1225-like predicted glycosylases |
| 结构域编号 domain_id | d1vkdd_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.4 — TM1225-like predicted glycosylases |
| 结构域编号 domain_id | d1vkde_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.4 — TM1225-like predicted glycosylases |
| 结构域编号 domain_id | d1vkdf_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.67 — 5-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.67.2 — Arabinanase/levansucrase/invertase |
| 家族 Family family | b.67.2.4 — TM1225-like predicted glycosylases |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1vkdA00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1vkdB00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1vkdC00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1vkdD00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1vkdE00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |
| 结构域编号 domain_id | 1vkdF00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 115 — 5 Propeller |
| 拓扑 Topology topology | 10 — Tachylectin-2; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Glycosyl hydrolase domain; family 43 |