1r3n
Crystal structure of beta-alanine synthase from Saccharomyces kluyveri
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 | 1r3n |
| 沉积日期 deposition_date | 2003-10-02 |
| 结构标题 title | Crystal structure of beta-alanine synthase from Saccharomyces kluyveri |
| 关键词 keywords | alpha and beta protein, di-zinc center, 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 | 61.23 Å |
| 回转半径 Rg (电子) rg_electron | 61.53 Å |
| 零角强度 I(0) i0 | 2176210000.00 |
| 分子量 molecular_weight | 383750.0 kDa |
| 排除体积 excluded_volume | 476180 ų |
| 包络体积 envelope_volume | 697740 ų |
| 水化壳体积 shell_volume | 98841 ų |
| 包络直径 envelope_diameter | 231.4 Å |
| 壳层 Rg shell_rg | 60.25 Å |
| 包络 Rg envelope_rg | 59.93 Å |
| 形状 Rg shape_rg | 61.54 Å |
| 总 Rg total_rg | 61.47 Å |
| 总原子数 total_atoms | 26978 |
| 残基数 n_residues | 3485 |
| 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 | 203.4 Å |
| Rg (实空间) rg_real | 61.43 Å |
| Rg 误差 (实空间) rg_real_error | 1.62 Å |
| I(0) (实空间) i0_real | 2.1760e+09 |
| I(0) 误差 (实空间) i0_real_error | 4.2310e+07 |
| Rg (倒空间) rg_reciprocal | 61.02 Å |
| I(0) (倒空间) i0_reciprocal | 2175000000.0000 |
| 解质量估计 total_estimate | 0.8512 |
| 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 | 70.4 Å |
| 偏度 Skewness skewness | 0.418 |
| 峰度 Kurtosis kurtosis | -0.058 |
| 角度范围 angular_range | — – 0.1300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0007 |
| 最高正则化参数 α highest_alpha | 41970000.0000 |
| 实空间数据点数 n_real_points | 27 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.471 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 32 domains
SCOP 2.08 (16 domains)
| 结构域编号 domain_id | d1r3na1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
| 结构域编号 domain_id | d1r3na2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.19 — Bacterial exopeptidase dimerisation domain |
| 家族 Family family | d.58.19.1 — Bacterial exopeptidase dimerisation domain |
| 结构域编号 domain_id | d1r3nb1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
| 结构域编号 domain_id | d1r3nb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.19 — Bacterial exopeptidase dimerisation domain |
| 家族 Family family | d.58.19.1 — Bacterial exopeptidase dimerisation domain |
| 结构域编号 domain_id | d1r3nc1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
| 结构域编号 domain_id | d1r3nc2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.19 — Bacterial exopeptidase dimerisation domain |
| 家族 Family family | d.58.19.1 — Bacterial exopeptidase dimerisation domain |
| 结构域编号 domain_id | d1r3nd1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
| 结构域编号 domain_id | d1r3nd2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.19 — Bacterial exopeptidase dimerisation domain |
| 家族 Family family | d.58.19.1 — Bacterial exopeptidase dimerisation domain |
| 结构域编号 domain_id | d1r3ne1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
| 结构域编号 domain_id | d1r3ne2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.19 — Bacterial exopeptidase dimerisation domain |
| 家族 Family family | d.58.19.1 — Bacterial exopeptidase dimerisation domain |
| 结构域编号 domain_id | d1r3nf1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
| 结构域编号 domain_id | d1r3nf2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.19 — Bacterial exopeptidase dimerisation domain |
| 家族 Family family | d.58.19.1 — Bacterial exopeptidase dimerisation domain |
| 结构域编号 domain_id | d1r3ng1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
| 结构域编号 domain_id | d1r3ng2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.19 — Bacterial exopeptidase dimerisation domain |
| 家族 Family family | d.58.19.1 — Bacterial exopeptidase dimerisation domain |
| 结构域编号 domain_id | d1r3nh1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.56 — Phosphorylase/hydrolase-like |
| 超家族 Superfamily superfamily | c.56.5 — Zn-dependent exopeptidases |
| 家族 Family family | c.56.5.4 — Bacterial dinuclear zinc exopeptidases |
| 结构域编号 domain_id | d1r3nh2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.19 — Bacterial exopeptidase dimerisation domain |
| 家族 Family family | d.58.19.1 — Bacterial exopeptidase dimerisation domain |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 1r3nA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1r3nA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 360 — |
| 结构域编号 domain_id | 1r3nB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1r3nB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 360 — |
| 结构域编号 domain_id | 1r3nC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1r3nC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 360 — |
| 结构域编号 domain_id | 1r3nD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1r3nD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 360 — |
| 结构域编号 domain_id | 1r3nE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1r3nE02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 360 — |
| 结构域编号 domain_id | 1r3nF01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1r3nF02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 360 — |
| 结构域编号 domain_id | 1r3nG01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1r3nG02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 360 — |
| 结构域编号 domain_id | 1r3nH01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 630 — Aminopeptidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Zn peptidases |
| 结构域编号 domain_id | 1r3nH02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 360 — |