2db4
Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae
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 | 2db4 |
| 沉积日期 deposition_date | 2005-12-15 |
| 结构标题 title | Crystal structure of rotor ring with DCCD of the V- ATPase from Enterococcus hirae |
| 关键词 keywords | ;NtpK, V-ATPase, Na(+)-ATPase, DCCD, Proteolipid, Enterococcus hirae, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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 | 37.06 Å |
| 回转半径 Rg (电子) rg_electron | 35.27 Å |
| 零角强度 I(0) i0 | 318902000.00 |
| 分子量 molecular_weight | 176410.0 kDa |
| 排除体积 excluded_volume | 234480 ų |
| 包络体积 envelope_volume | 282390 ų |
| 水化壳体积 shell_volume | 63079 ų |
| 包络直径 envelope_diameter | 101.1 Å |
| 壳层 Rg shell_rg | 45.11 Å |
| 包络 Rg envelope_rg | 33.94 Å |
| 形状 Rg shape_rg | 35.29 Å |
| 总 Rg total_rg | 35.95 Å |
| 总原子数 total_atoms | 12404 |
| 残基数 n_residues | 1560 |
| 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 | 101.3 Å |
| Rg (实空间) rg_real | 36.62 Å |
| Rg 误差 (实空间) rg_real_error | 0.51 Å |
| I(0) (实空间) i0_real | 3.1890e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.5170e+06 |
| Rg (倒空间) rg_reciprocal | 36.89 Å |
| I(0) (倒空间) i0_reciprocal | 319000000.0000 |
| 解质量估计 total_estimate | 0.8518 |
| 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 | 58.9 Å |
| 偏度 Skewness skewness | -0.306 |
| 峰度 Kurtosis kurtosis | -0.592 |
| 角度范围 angular_range | — – 0.2150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 36550000.0000 |
| 实空间数据点数 n_real_points | 44 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.855 |
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) 10 domains
CATH v4.4 (10 domains)
| 结构域编号 domain_id | 2db4A00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4B00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4C00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4D00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4E00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4F00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4G00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4H00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4I00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |
| 结构域编号 domain_id | 2db4J00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 610 — lithium bound rotor ring of v- atpase |