1xm5
Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054
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 | 1xm5 |
| 沉积日期 deposition_date | 2004-10-01 |
| 结构标题 title | Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054 |
| 关键词 keywords | ;Structural genomics, protein structure initiative, NYSGXRC target T842, PFAM family UPF0054, PSI, New York SGX Research Center for Structural Genomics, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION |
| 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 | 27.00 Å |
| 回转半径 Rg (电子) rg_electron | 25.93 Å |
| 零角强度 I(0) i0 | 80292400.00 |
| 分子量 molecular_weight | 68229.0 kDa |
| 排除体积 excluded_volume | 84586 ų |
| 包络体积 envelope_volume | 106370 ų |
| 水化壳体积 shell_volume | 33741 ų |
| 包络直径 envelope_diameter | 78.9 Å |
| 壳层 Rg shell_rg | 33.79 Å |
| 包络 Rg envelope_rg | 25.43 Å |
| 形状 Rg shape_rg | 25.95 Å |
| 总 Rg total_rg | 26.73 Å |
| 总原子数 total_atoms | 4781 |
| 残基数 n_residues | 604 |
| 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 | 79.6 Å |
| Rg (实空间) rg_real | 26.81 Å |
| Rg 误差 (实空间) rg_real_error | 0.39 Å |
| I(0) (实空间) i0_real | 8.0290e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.0960e+06 |
| Rg (倒空间) rg_reciprocal | 26.87 Å |
| I(0) (倒空间) i0_reciprocal | 80300000.0000 |
| 解质量估计 total_estimate | 0.9114 |
| 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 | 35.1 Å |
| 偏度 Skewness skewness | 0.091 |
| 峰度 Kurtosis kurtosis | -0.579 |
| 角度范围 angular_range | — – 0.2950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 21680000.0000 |
| 实空间数据点数 n_real_points | 60 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.972; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.941 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1xm5a_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.92 — Zincin-like |
| 超家族 Superfamily superfamily | d.92.1 — Metalloproteases ('zincins'), catalytic domain |
| 家族 Family family | d.92.1.15 — Predicted metal-dependent hydrolase |
| 结构域编号 domain_id | d1xm5b_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.92 — Zincin-like |
| 超家族 Superfamily superfamily | d.92.1 — Metalloproteases ('zincins'), catalytic domain |
| 家族 Family family | d.92.1.15 — Predicted metal-dependent hydrolase |
| 结构域编号 domain_id | d1xm5c_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.92 — Zincin-like |
| 超家族 Superfamily superfamily | d.92.1 — Metalloproteases ('zincins'), catalytic domain |
| 家族 Family family | d.92.1.15 — Predicted metal-dependent hydrolase |
| 结构域编号 domain_id | d1xm5d_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.92 — Zincin-like |
| 超家族 Superfamily superfamily | d.92.1 — Metalloproteases ('zincins'), catalytic domain |
| 家族 Family family | d.92.1.15 — Predicted metal-dependent hydrolase |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1xm5A00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Metalloproteases ("zincins"), catalytic domain |
| 结构域编号 domain_id | 1xm5B00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Metalloproteases ("zincins"), catalytic domain |
| 结构域编号 domain_id | 1xm5C00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Metalloproteases ("zincins"), catalytic domain |
| 结构域编号 domain_id | 1xm5D00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 390 — Collagenase (Catalytic Domain) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Metalloproteases ("zincins"), catalytic domain |