1kji
Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-AMPPCP
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 | 1kji |
| 沉积日期 deposition_date | 2001-12-04 |
| 结构标题 title | Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-AMPPCP |
| 关键词 keywords | ATP-grasp, purine biosynthesis, nucleotide, 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 | 29.13 Å |
| 回转半径 Rg (电子) rg_electron | 28.47 Å |
| 零角强度 I(0) i0 | 120004000.00 |
| 分子量 molecular_weight | 85812.0 kDa |
| 排除体积 excluded_volume | 107030 ų |
| 包络体积 envelope_volume | 125850 ų |
| 水化壳体积 shell_volume | 37319 ų |
| 包络直径 envelope_diameter | 109.6 Å |
| 壳层 Rg shell_rg | 35.49 Å |
| 包络 Rg envelope_rg | 28.74 Å |
| 形状 Rg shape_rg | 28.47 Å |
| 总 Rg total_rg | 29.04 Å |
| 总原子数 total_atoms | 6017 |
| 残基数 n_residues | 778 |
| 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 | 104.9 Å |
| Rg (实空间) rg_real | 29.24 Å |
| Rg 误差 (实空间) rg_real_error | 0.95 Å |
| I(0) (实空间) i0_real | 1.2000e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.1220e+06 |
| Rg (倒空间) rg_reciprocal | 29.19 Å |
| I(0) (倒空间) i0_reciprocal | 120000000.0000 |
| 解质量估计 total_estimate | 0.8292 |
| 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 | 33.0 Å |
| 偏度 Skewness skewness | 0.573 |
| 峰度 Kurtosis kurtosis | 0.145 |
| 角度范围 angular_range | — – 0.2700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 35050000.0000 |
| 实空间数据点数 n_real_points | 55 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.620; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.953 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1kjia1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.84 — Barrel-sandwich hybrid |
| 超家族 Superfamily superfamily | b.84.2 — Rudiment single hybrid motif |
| 家族 Family family | b.84.2.1 — BC C-terminal domain-like |
| 结构域编号 domain_id | d1kjia2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.30 — PreATP-grasp domain |
| 超家族 Superfamily superfamily | c.30.1 — PreATP-grasp domain |
| 家族 Family family | c.30.1.1 — BC N-terminal domain-like |
| 结构域编号 domain_id | d1kjia3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.142 — ATP-grasp |
| 超家族 Superfamily superfamily | d.142.1 — Glutathione synthetase ATP-binding domain-like |
| 家族 Family family | d.142.1.2 — BC ATP-binding domain-like |
| 结构域编号 domain_id | d1kjib1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.84 — Barrel-sandwich hybrid |
| 超家族 Superfamily superfamily | b.84.2 — Rudiment single hybrid motif |
| 家族 Family family | b.84.2.1 — BC C-terminal domain-like |
| 结构域编号 domain_id | d1kjib2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.30 — PreATP-grasp domain |
| 超家族 Superfamily superfamily | c.30.1 — PreATP-grasp domain |
| 家族 Family family | c.30.1.1 — BC N-terminal domain-like |
| 结构域编号 domain_id | d1kjib3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.142 — ATP-grasp |
| 超家族 Superfamily superfamily | d.142.1 — Glutathione synthetase ATP-binding domain-like |
| 家族 Family family | d.142.1.2 — BC ATP-binding domain-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1kjiA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1kjiA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, A domain |
| 结构域编号 domain_id | 1kjiA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 470 — D-amino Acid Aminotransferase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, B domain |
| 结构域编号 domain_id | 1kjiB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1kjiB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, A domain |
| 结构域编号 domain_id | 1kjiB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 470 — D-amino Acid Aminotransferase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, B domain |