1s20
;A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82 ;
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 | 1s20 |
| 沉积日期 deposition_date | 2004-01-07 |
| 结构标题 title | ;A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82 ; |
| 关键词 keywords | ;alpha beta dimeric protein, OXIDOREDUCTASE, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG ;; OXIDOREDUCTASE |
| 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 | 57.82 Å |
| 回转半径 Rg (电子) rg_electron | 58.39 Å |
| 零角强度 I(0) i0 | 1482580000.00 |
| 分子量 molecular_weight | 304940.0 kDa |
| 排除体积 excluded_volume | 372510 ų |
| 包络体积 envelope_volume | 501380 ų |
| 水化壳体积 shell_volume | 74623 ų |
| 包络直径 envelope_diameter | 205.9 Å |
| 壳层 Rg shell_rg | 55.95 Å |
| 包络 Rg envelope_rg | 57.51 Å |
| 形状 Rg shape_rg | 58.43 Å |
| 总 Rg total_rg | 58.18 Å |
| 总原子数 total_atoms | 20957 |
| 残基数 n_residues | 2552 |
| 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 | 206.5 Å |
| Rg (实空间) rg_real | 58.31 Å |
| Rg 误差 (实空间) rg_real_error | 2.57 Å |
| I(0) (实空间) i0_real | 1.4830e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.9100e+07 |
| Rg (倒空间) rg_reciprocal | 57.37 Å |
| I(0) (倒空间) i0_reciprocal | 1480000000.0000 |
| 解质量估计 total_estimate | 0.7919 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 45.9 Å |
| 偏度 Skewness skewness | 0.442 |
| 峰度 Kurtosis kurtosis | -0.554 |
| 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 | 71400000.0000 |
| 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: 0.678; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.626; Smooth: 0.631 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 40 domains
SCOP 2.08 (16 domains)
| 结构域编号 domain_id | d1s20a1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.122 — L-sulfolactate dehydrogenase-like |
| 超家族 Superfamily superfamily | c.122.1 — L-sulfolactate dehydrogenase-like |
| 家族 Family family | c.122.1.1 — L-sulfolactate dehydrogenase-like |
| 结构域编号 domain_id | d1s20a2 |
| 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 | d1s20b1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.122 — L-sulfolactate dehydrogenase-like |
| 超家族 Superfamily superfamily | c.122.1 — L-sulfolactate dehydrogenase-like |
| 家族 Family family | c.122.1.1 — L-sulfolactate dehydrogenase-like |
| 结构域编号 domain_id | d1s20b2 |
| 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 | d1s20c1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.122 — L-sulfolactate dehydrogenase-like |
| 超家族 Superfamily superfamily | c.122.1 — L-sulfolactate dehydrogenase-like |
| 家族 Family family | c.122.1.1 — L-sulfolactate dehydrogenase-like |
| 结构域编号 domain_id | d1s20c2 |
| 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 | d1s20d1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.122 — L-sulfolactate dehydrogenase-like |
| 超家族 Superfamily superfamily | c.122.1 — L-sulfolactate dehydrogenase-like |
| 家族 Family family | c.122.1.1 — L-sulfolactate dehydrogenase-like |
| 结构域编号 domain_id | d1s20d2 |
| 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 | d1s20e1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.122 — L-sulfolactate dehydrogenase-like |
| 超家族 Superfamily superfamily | c.122.1 — L-sulfolactate dehydrogenase-like |
| 家族 Family family | c.122.1.1 — L-sulfolactate dehydrogenase-like |
| 结构域编号 domain_id | d1s20e2 |
| 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 | d1s20f1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.122 — L-sulfolactate dehydrogenase-like |
| 超家族 Superfamily superfamily | c.122.1 — L-sulfolactate dehydrogenase-like |
| 家族 Family family | c.122.1.1 — L-sulfolactate dehydrogenase-like |
| 结构域编号 domain_id | d1s20f2 |
| 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 | d1s20g1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.122 — L-sulfolactate dehydrogenase-like |
| 超家族 Superfamily superfamily | c.122.1 — L-sulfolactate dehydrogenase-like |
| 家族 Family family | c.122.1.1 — L-sulfolactate dehydrogenase-like |
| 结构域编号 domain_id | d1s20g2 |
| 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 | d1s20h1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.122 — L-sulfolactate dehydrogenase-like |
| 超家族 Superfamily superfamily | c.122.1 — L-sulfolactate dehydrogenase-like |
| 家族 Family family | c.122.1.1 — L-sulfolactate dehydrogenase-like |
| 结构域编号 domain_id | d1s20h2 |
| 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 |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 1s20A01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel |
| 结构域编号 domain_id | 1s20A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain |
| 结构域编号 domain_id | 1s20A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 60 — Wheat Germ Agglutinin (Isolectin 2); domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hypothetical oxidoreductase yiak; domain 3 |
| 结构域编号 domain_id | 1s20B01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel |
| 结构域编号 domain_id | 1s20B02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain |
| 结构域编号 domain_id | 1s20B03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 60 — Wheat Germ Agglutinin (Isolectin 2); domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hypothetical oxidoreductase yiak; domain 3 |
| 结构域编号 domain_id | 1s20C01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel |
| 结构域编号 domain_id | 1s20C02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain |
| 结构域编号 domain_id | 1s20C03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 60 — Wheat Germ Agglutinin (Isolectin 2); domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hypothetical oxidoreductase yiak; domain 3 |
| 结构域编号 domain_id | 1s20D01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel |
| 结构域编号 domain_id | 1s20D02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain |
| 结构域编号 domain_id | 1s20D03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 60 — Wheat Germ Agglutinin (Isolectin 2); domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hypothetical oxidoreductase yiak; domain 3 |
| 结构域编号 domain_id | 1s20E01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel |
| 结构域编号 domain_id | 1s20E02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain |
| 结构域编号 domain_id | 1s20E03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 60 — Wheat Germ Agglutinin (Isolectin 2); domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hypothetical oxidoreductase yiak; domain 3 |
| 结构域编号 domain_id | 1s20F01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel |
| 结构域编号 domain_id | 1s20F02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain |
| 结构域编号 domain_id | 1s20F03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 60 — Wheat Germ Agglutinin (Isolectin 2); domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hypothetical oxidoreductase yiak; domain 3 |
| 结构域编号 domain_id | 1s20G01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel |
| 结构域编号 domain_id | 1s20G02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain |
| 结构域编号 domain_id | 1s20G03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 60 — Wheat Germ Agglutinin (Isolectin 2); domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hypothetical oxidoreductase yiak; domain 3 |
| 结构域编号 domain_id | 1s20H01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel |
| 结构域编号 domain_id | 1s20H02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1370 — Ribosomal Protein S8; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain |
| 结构域编号 domain_id | 1s20H03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 60 — Wheat Germ Agglutinin (Isolectin 2); domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hypothetical oxidoreductase yiak; domain 3 |