2cyd
Crystal structure of Lithium bound rotor ring 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 | 2cyd |
| 沉积日期 deposition_date | 2005-07-06 |
| 结构标题 title | Crystal structure of Lithium bound rotor ring of the V-ATPase from Enterococcus hirae |
| 关键词 keywords | ;NtpK, V-ATPase, Na(+)-ATPase, Lithium, Proteolipid, Enterococcus, 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 | 36.77 Å |
| 回转半径 Rg (电子) rg_electron | 34.99 Å |
| 零角强度 I(0) i0 | 331915000.00 |
| 分子量 molecular_weight | 174340.0 kDa |
| 排除体积 excluded_volume | 229800 ų |
| 包络体积 envelope_volume | 276210 ų |
| 水化壳体积 shell_volume | 62179 ų |
| 包络直径 envelope_diameter | 101.8 Å |
| 壳层 Rg shell_rg | 44.77 Å |
| 包络 Rg envelope_rg | 33.71 Å |
| 形状 Rg shape_rg | 35.04 Å |
| 总 Rg total_rg | 35.56 Å |
| 总原子数 total_atoms | 12248 |
| 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 | 102.0 Å |
| Rg (实空间) rg_real | 36.35 Å |
| Rg 误差 (实空间) rg_real_error | 0.43 Å |
| I(0) (实空间) i0_real | 3.3190e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.7660e+06 |
| Rg (倒空间) rg_reciprocal | 36.61 Å |
| I(0) (倒空间) i0_reciprocal | 332000000.0000 |
| 解质量估计 total_estimate | 0.8651 |
| 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 | 56.9 Å |
| 偏度 Skewness skewness | -0.278 |
| 峰度 Kurtosis kurtosis | -0.599 |
| 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 | 33430000.0000 |
| 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: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.923 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 10 domains
CATH v4.4 (10 domains)
| 结构域编号 domain_id | 2cydA00 |
| 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 | 2cydB00 |
| 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 | 2cydC00 |
| 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 | 2cydD00 |
| 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 | 2cydE00 |
| 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 | 2cydF00 |
| 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 | 2cydG00 |
| 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 | 2cydH00 |
| 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 | 2cydI00 |
| 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 | 2cydJ00 |
| 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 |