1nmd
Crystal Structure of D. Discoideum Actin-Gelsolin Segment 1 Complex Crystallized In Presence Of Lithium ATP
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 | 1nmd |
| 沉积日期 deposition_date | 2003-01-09 |
| 结构标题 title | Crystal Structure of D. Discoideum Actin-Gelsolin Segment 1 Complex Crystallized In Presence Of Lithium ATP |
| 关键词 keywords | ACTIN, GELSOLIN, CYTOSKELETON ORGANIZATION, ACTIN-ASSOCIATED PROTEIN, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN |
| 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 | 24.82 Å |
| 回转半径 Rg (电子) rg_electron | 23.96 Å |
| 零角强度 I(0) i0 | 49062300.00 |
| 分子量 molecular_weight | 54051.0 kDa |
| 排除体积 excluded_volume | 67375 ų |
| 包络体积 envelope_volume | 77977 ų |
| 水化壳体积 shell_volume | 27264 ų |
| 包络直径 envelope_diameter | 84.8 Å |
| 壳层 Rg shell_rg | 31.16 Å |
| 包络 Rg envelope_rg | 24.25 Å |
| 形状 Rg shape_rg | 23.98 Å |
| 总 Rg total_rg | 24.67 Å |
| 总原子数 total_atoms | 3799 |
| 残基数 n_residues | 485 |
| 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 | 84.4 Å |
| Rg (实空间) rg_real | 24.78 Å |
| Rg 误差 (实空间) rg_real_error | 0.75 Å |
| I(0) (实空间) i0_real | 4.9060e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.2980e+05 |
| Rg (倒空间) rg_reciprocal | 24.79 Å |
| I(0) (倒空间) i0_reciprocal | 49060000.0000 |
| 解质量估计 total_estimate | 0.7839 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 4 |
| 主峰位置 r_peak_primary | 28.1 Å |
| 偏度 Skewness skewness | 0.319 |
| 峰度 Kurtosis kurtosis | -0.330 |
| 角度范围 angular_range | — – 0.3200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 12970000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.767; Stabil: 0.973; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 7 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1nmda1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.1 — Actin/HSP70 |
| 结构域编号 domain_id | d1nmda2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.1 — Actin/HSP70 |
| 结构域编号 domain_id | d1nmdg_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.109 — Gelsolin-like |
| 超家族 Superfamily superfamily | d.109.1 — Actin depolymerizing proteins |
| 家族 Family family | d.109.1.1 — Gelsolin-like |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1nmdA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — ATPase, nucleotide binding domain |
| 结构域编号 domain_id | 1nmdA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — ATPase, nucleotide binding domain |
| 结构域编号 domain_id | 1nmdA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 640 — Actin; Chain A, domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — ATPase, substrate binding domain, subdomain 4 |
| 结构域编号 domain_id | 1nmdG00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 20 — Severin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Severin |