2g8y
The structure of a putative malate/lactate dehydrogenase from E. coli.
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 | 2g8y |
| 沉积日期 deposition_date | 2006-03-03 |
| 结构标题 title | The structure of a putative malate/lactate dehydrogenase from E. coli. |
| 关键词 keywords | ;malate, lactate, dehydrogenase, NAD, E.coli, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, OXIDOREDUCTASE ;; 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 | 27.16 Å |
| 回转半径 Rg (电子) rg_electron | 26.29 Å |
| 零角强度 I(0) i0 | 116736000.00 |
| 分子量 molecular_weight | 80922.0 kDa |
| 排除体积 excluded_volume | 98970 ų |
| 包络体积 envelope_volume | 116150 ų |
| 水化壳体积 shell_volume | 36074 ų |
| 包络直径 envelope_diameter | 107.3 Å |
| 壳层 Rg shell_rg | 34.21 Å |
| 包络 Rg envelope_rg | 26.74 Å |
| 形状 Rg shape_rg | 26.31 Å |
| 总 Rg total_rg | 26.93 Å |
| 总原子数 total_atoms | 5622 |
| 残基数 n_residues | 701 |
| 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 | 99.3 Å |
| Rg (实空间) rg_real | 27.17 Å |
| Rg 误差 (实空间) rg_real_error | 0.83 Å |
| I(0) (实空间) i0_real | 1.1670e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.9980e+06 |
| Rg (倒空间) rg_reciprocal | 27.17 Å |
| I(0) (倒空间) i0_reciprocal | 116700000.0000 |
| 解质量估计 total_estimate | 0.8300 |
| 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 | 30.8 Å |
| 偏度 Skewness skewness | 0.472 |
| 峰度 Kurtosis kurtosis | 0.085 |
| 角度范围 angular_range | — – 0.2900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 30190000.0000 |
| 实空间数据点数 n_real_points | 59 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.613; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.973 |
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) 8 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2g8ya_ |
| 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.122.1.0 — automated matches |
| 结构域编号 domain_id | d2g8yb_ |
| 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.122.1.0 — automated matches |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2g8yA01 |
| 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 | 2g8yA02 |
| 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 | 2g8yA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 460 — Single helix bin |
| 结构域编号 domain_id | 2g8yB01 |
| 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 | 2g8yB02 |
| 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 | 2g8yB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 460 — Single helix bin |