1rxq
YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology
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 | 1rxq |
| 沉积日期 deposition_date | 2003-12-18 |
| 结构标题 title | YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology |
| 关键词 keywords | ;Nickel-binding, hydrolase, helix-bundle, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, metal-binding protein, METAL BINDING PROTEIN ;; METAL BINDING 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 | 34.23 Å |
| 回转半径 Rg (电子) rg_electron | 33.91 Å |
| 零角强度 I(0) i0 | 107827000.00 |
| 分子量 molecular_weight | 81788.0 kDa |
| 排除体积 excluded_volume | 101580 ų |
| 包络体积 envelope_volume | 130500 ų |
| 水化壳体积 shell_volume | 33131 ų |
| 包络直径 envelope_diameter | 111.8 Å |
| 壳层 Rg shell_rg | 39.12 Å |
| 包络 Rg envelope_rg | 33.75 Å |
| 形状 Rg shape_rg | 33.90 Å |
| 总 Rg total_rg | 34.35 Å |
| 总原子数 total_atoms | 5731 |
| 残基数 n_residues | 680 |
| 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 | 112.1 Å |
| Rg (实空间) rg_real | 34.40 Å |
| Rg 误差 (实空间) rg_real_error | 0.75 Å |
| I(0) (实空间) i0_real | 1.0780e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.5600e+06 |
| Rg (倒空间) rg_reciprocal | 34.30 Å |
| I(0) (倒空间) i0_reciprocal | 107800000.0000 |
| 解质量估计 total_estimate | 0.8497 |
| 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 | 29.2 Å |
| 偏度 Skewness skewness | 0.364 |
| 峰度 Kurtosis kurtosis | -0.761 |
| 角度范围 angular_range | — – 0.2300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 19020000.0000 |
| 实空间数据点数 n_real_points | 47 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.828; Smooth: 0.909 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (8)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1rxqa_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.213 — DinB/YfiT-like putative metalloenzymes |
| 超家族 Superfamily superfamily | a.213.1 — DinB/YfiT-like putative metalloenzymes |
| 家族 Family family | a.213.1.1 — YfiT-like putative metal-dependent hydrolases |
| 结构域编号 domain_id | d1rxqb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.213 — DinB/YfiT-like putative metalloenzymes |
| 超家族 Superfamily superfamily | a.213.1 — DinB/YfiT-like putative metalloenzymes |
| 家族 Family family | a.213.1.1 — YfiT-like putative metal-dependent hydrolases |
| 结构域编号 domain_id | d1rxqc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.213 — DinB/YfiT-like putative metalloenzymes |
| 超家族 Superfamily superfamily | a.213.1 — DinB/YfiT-like putative metalloenzymes |
| 家族 Family family | a.213.1.1 — YfiT-like putative metal-dependent hydrolases |
| 结构域编号 domain_id | d1rxqd_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.213 — DinB/YfiT-like putative metalloenzymes |
| 超家族 Superfamily superfamily | a.213.1 — DinB/YfiT-like putative metalloenzymes |
| 家族 Family family | a.213.1.1 — YfiT-like putative metal-dependent hydrolases |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1rxqA00 |
| 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 | 450 — dinb family like domain |
| 结构域编号 domain_id | 1rxqB00 |
| 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 | 450 — dinb family like domain |
| 结构域编号 domain_id | 1rxqC00 |
| 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 | 450 — dinb family like domain |
| 结构域编号 domain_id | 1rxqD00 |
| 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 | 450 — dinb family like domain |