1ofd
Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom resolution
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 | 1ofd |
| 沉积日期 deposition_date | 2003-04-14 |
| 结构标题 title | Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate at 2.0 Angstrom resolution |
| 关键词 keywords | OXIDOREDUCTASE, COMPLEX ENZYME, SUBSTRATE CHANNELING, AMIDOTRANSFERASE, FLAVOPROTEIN, IRON-SULPHUR, FD-GOGAT; OXIDOREDUCTASE |
| 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 | 56.90 Å |
| 回转半径 Rg (电子) rg_electron | 57.18 Å |
| 零角强度 I(0) i0 | 1536200000.00 |
| 分子量 molecular_weight | 326920.0 kDa |
| 排除体积 excluded_volume | 408160 ų |
| 包络体积 envelope_volume | 539410 ų |
| 水化壳体积 shell_volume | 78425 ų |
| 包络直径 envelope_diameter | 189.3 Å |
| 壳层 Rg shell_rg | 58.66 Å |
| 包络 Rg envelope_rg | 56.12 Å |
| 形状 Rg shape_rg | 57.19 Å |
| 总 Rg total_rg | 57.19 Å |
| 总原子数 total_atoms | 22964 |
| 残基数 n_residues | 2982 |
| 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 | 176.3 Å |
| Rg (实空间) rg_real | 57.26 Å |
| Rg 误差 (实空间) rg_real_error | 1.87 Å |
| I(0) (实空间) i0_real | 1.5360e+09 |
| I(0) 误差 (实空间) i0_real_error | 3.0730e+07 |
| Rg (倒空间) rg_reciprocal | 56.55 Å |
| I(0) (倒空间) i0_reciprocal | 1534000000.0000 |
| 解质量估计 total_estimate | 0.7704 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 44.1 Å |
| 偏度 Skewness skewness | 0.354 |
| 峰度 Kurtosis kurtosis | -0.843 |
| 角度范围 angular_range | — – 0.1400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 186500000.0000 |
| 实空间数据点数 n_real_points | 29 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.707; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.013 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1ofda1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.80 — Single-stranded right-handed beta-helix |
| 超家族 Superfamily superfamily | b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain |
| 家族 Family family | b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain |
| 结构域编号 domain_id | d1ofda2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.4 — FMN-linked oxidoreductases |
| 家族 Family family | c.1.4.1 — FMN-linked oxidoreductases |
| 结构域编号 domain_id | d1ofda3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.153 — Ntn hydrolase-like |
| 超家族 Superfamily superfamily | d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases) |
| 家族 Family family | d.153.1.1 — Class II glutamine amidotransferases |
| 结构域编号 domain_id | d1ofdb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.80 — Single-stranded right-handed beta-helix |
| 超家族 Superfamily superfamily | b.80.4 — Alpha subunit of glutamate synthase, C-terminal domain |
| 家族 Family family | b.80.4.1 — Alpha subunit of glutamate synthase, C-terminal domain |
| 结构域编号 domain_id | d1ofdb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.4 — FMN-linked oxidoreductases |
| 家族 Family family | c.1.4.1 — FMN-linked oxidoreductases |
| 结构域编号 domain_id | d1ofdb3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.153 — Ntn hydrolase-like |
| 超家族 Superfamily superfamily | d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases) |
| 家族 Family family | d.153.1.1 — Class II glutamine amidotransferases |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1ofdA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 60 — 4-Layer Sandwich |
| 拓扑 Topology topology | 20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain |
| 结构域编号 domain_id | 1ofdA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 70 — Aldolase class I |
| 结构域编号 domain_id | 1ofdA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 70 — Aldolase class I |
| 结构域编号 domain_id | 1ofdA04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 160 — 3 Solenoid |
| 拓扑 Topology topology | 20 — Pectate Lyase C-like |
| 同源超家族 H-superfamily homologous superfamily | 60 — Glutamate synthase, alpha subunit, C-terminal domain |
| 结构域编号 domain_id | 1ofdB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 60 — 4-Layer Sandwich |
| 拓扑 Topology topology | 20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain |
| 结构域编号 domain_id | 1ofdB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 70 — Aldolase class I |
| 结构域编号 domain_id | 1ofdB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 70 — Aldolase class I |
| 结构域编号 domain_id | 1ofdB04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 160 — 3 Solenoid |
| 拓扑 Topology topology | 20 — Pectate Lyase C-like |
| 同源超家族 H-superfamily homologous superfamily | 60 — Glutamate synthase, alpha subunit, C-terminal domain |