2j5r
;2.25 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui after second radiation burn (radiation damage series) ;
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 | 2j5r |
| 沉积日期 deposition_date | 2006-09-19 |
| 结构标题 title | ;2.25 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui after second radiation burn (radiation damage series) ; |
| 关键词 keywords | NAD, HALOPHILE, OXIDOREDUCTASE, RADIATION DAMAGE, MALATE DEHYDROGENASE, TRICARBOXYLIC ACID CYCLE; 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 | 31.76 Å |
| 回转半径 Rg (电子) rg_electron | 30.62 Å |
| 零角强度 I(0) i0 | 287601000.00 |
| 分子量 molecular_weight | 128630.0 kDa |
| 排除体积 excluded_volume | 157850 ų |
| 包络体积 envelope_volume | 195070 ų |
| 水化壳体积 shell_volume | 50642 ų |
| 包络直径 envelope_diameter | 94.9 Å |
| 壳层 Rg shell_rg | 39.64 Å |
| 包络 Rg envelope_rg | 30.46 Å |
| 形状 Rg shape_rg | 30.63 Å |
| 总 Rg total_rg | 31.29 Å |
| 总原子数 total_atoms | 9059 |
| 残基数 n_residues | 1182 |
| 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 | 95.0 Å |
| Rg (实空间) rg_real | 31.50 Å |
| Rg 误差 (实空间) rg_real_error | 0.55 Å |
| I(0) (实空间) i0_real | 2.8760e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.4710e+06 |
| Rg (倒空间) rg_reciprocal | 31.61 Å |
| I(0) (倒空间) i0_reciprocal | 287600000.0000 |
| 解质量估计 total_estimate | 0.9088 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 41.8 Å |
| 偏度 Skewness skewness | 0.052 |
| 峰度 Kurtosis kurtosis | -0.605 |
| 角度范围 angular_range | — – 0.2500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 74080000.0000 |
| 实空间数据点数 n_real_points | 51 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.987 |
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) 16 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d2j5ra1 |
| 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 | d2j5ra2 |
| 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.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain |
| 结构域编号 domain_id | d2j5rb1 |
| 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 | d2j5rb2 |
| 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.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain |
| 结构域编号 domain_id | d2j5rc1 |
| 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 | d2j5rc2 |
| 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.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain |
| 结构域编号 domain_id | d2j5rd1 |
| 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 | d2j5rd2 |
| 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.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 2j5rA01 |
| 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 | 2j5rA02 |
| 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 | 2j5rB01 |
| 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 | 2j5rB02 |
| 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 | 2j5rC01 |
| 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 | 2j5rC02 |
| 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 | 2j5rD01 |
| 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 | 2j5rD02 |
| 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 |