1khd
;Crystal Structure Analysis of the anthranilate phosphoribosyltransferase from Erwinia carotovora at 1.9 resolution (current name, Pectobacterium carotovorum) ;
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 | 1khd |
| 沉积日期 deposition_date | 2001-11-29 |
| 结构标题 title | ;Crystal Structure Analysis of the anthranilate phosphoribosyltransferase from Erwinia carotovora at 1.9 resolution (current name, Pectobacterium carotovorum) ; |
| 关键词 keywords | type 3 prt fold, nucleotide binding fold, TRANSFERASE; TRANSFERASE |
| 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 | 40.91 Å |
| 回转半径 Rg (电子) rg_electron | 40.13 Å |
| 零角强度 I(0) i0 | 293195000.00 |
| 分子量 molecular_weight | 138200.0 kDa |
| 排除体积 excluded_volume | 172360 ų |
| 包络体积 envelope_volume | 233380 ų |
| 水化壳体积 shell_volume | 47670 ų |
| 包络直径 envelope_diameter | 127.9 Å |
| 壳层 Rg shell_rg | 46.91 Å |
| 包络 Rg envelope_rg | 38.85 Å |
| 形状 Rg shape_rg | 40.15 Å |
| 总 Rg total_rg | 40.42 Å |
| 总原子数 total_atoms | 9732 |
| 残基数 n_residues | 1301 |
| 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 | 128.8 Å |
| Rg (实空间) rg_real | 40.82 Å |
| Rg 误差 (实空间) rg_real_error | 1.06 Å |
| I(0) (实空间) i0_real | 2.9320e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.8230e+06 |
| Rg (倒空间) rg_reciprocal | 40.91 Å |
| I(0) (倒空间) i0_reciprocal | 293200000.0000 |
| 解质量估计 total_estimate | 0.8972 |
| 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 | 59.5 Å |
| 偏度 Skewness skewness | 0.094 |
| 峰度 Kurtosis kurtosis | -0.725 |
| 角度范围 angular_range | — – 0.1950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 45960000.0000 |
| 实空间数据点数 n_real_points | 40 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.861 |
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) 16 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d1khda1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.46 — Methionine synthase domain-like |
| 超家族 Superfamily superfamily | a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain |
| 家族 Family family | a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain |
| 结构域编号 domain_id | d1khda2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 超家族 Superfamily superfamily | c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 家族 Family family | c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 结构域编号 domain_id | d1khdb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.46 — Methionine synthase domain-like |
| 超家族 Superfamily superfamily | a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain |
| 家族 Family family | a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain |
| 结构域编号 domain_id | d1khdb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 超家族 Superfamily superfamily | c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 家族 Family family | c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 结构域编号 domain_id | d1khdc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.46 — Methionine synthase domain-like |
| 超家族 Superfamily superfamily | a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain |
| 家族 Family family | a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain |
| 结构域编号 domain_id | d1khdc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 超家族 Superfamily superfamily | c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 家族 Family family | c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 结构域编号 domain_id | d1khdd1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.46 — Methionine synthase domain-like |
| 超家族 Superfamily superfamily | a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain |
| 家族 Family family | a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain |
| 结构域编号 domain_id | d1khdd2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 超家族 Superfamily superfamily | c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 家族 Family family | c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1khdA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C |
| 结构域编号 domain_id | 1khdA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 结构域编号 domain_id | 1khdB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C |
| 结构域编号 domain_id | 1khdB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 结构域编号 domain_id | 1khdC01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C |
| 结构域编号 domain_id | 1khdC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |
| 结构域编号 domain_id | 1khdD01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C |
| 结构域编号 domain_id | 1khdD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain |