1t5o
Crystal structure of the translation initiation factor eIF-2B, subunit delta, from A. fulgidus
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 | 1t5o |
| 沉积日期 deposition_date | 2004-05-04 |
| 结构标题 title | Crystal structure of the translation initiation factor eIF-2B, subunit delta, from A. fulgidus |
| 关键词 keywords | ;translation initiation factor, subunit delta, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, translation ;; TRANSLATION |
| 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 | 38.89 Å |
| 回转半径 Rg (电子) rg_electron | 38.35 Å |
| 零角强度 I(0) i0 | 328668000.00 |
| 分子量 molecular_weight | 150690.0 kDa |
| 排除体积 excluded_volume | 190230 ų |
| 包络体积 envelope_volume | 238500 ų |
| 水化壳体积 shell_volume | 52663 ų |
| 包络直径 envelope_diameter | 135.7 Å |
| 壳层 Rg shell_rg | 42.89 Å |
| 包络 Rg envelope_rg | 38.69 Å |
| 形状 Rg shape_rg | 38.36 Å |
| 总 Rg total_rg | 38.57 Å |
| 总原子数 total_atoms | 10604 |
| 残基数 n_residues | 1360 |
| 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 | 126.4 Å |
| Rg (实空间) rg_real | 38.91 Å |
| Rg 误差 (实空间) rg_real_error | 1.06 Å |
| I(0) (实空间) i0_real | 3.2870e+08 |
| I(0) 误差 (实空间) i0_real_error | 6.2200e+06 |
| Rg (倒空间) rg_reciprocal | 38.90 Å |
| I(0) (倒空间) i0_reciprocal | 328700000.0000 |
| 解质量估计 total_estimate | 0.6904 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 43.2 Å |
| 偏度 Skewness skewness | 0.297 |
| 峰度 Kurtosis kurtosis | -0.485 |
| 角度范围 angular_range | — – 0.2050 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 72540000.0000 |
| 实空间数据点数 n_real_points | 42 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 0.132; Positv: 1.000; Valcen: 0.991; Smooth: 0.795 |
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 | d1t5oa1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.124 — NagB/RpiA/CoA transferase-like |
| 超家族 Superfamily superfamily | c.124.1 — NagB/RpiA/CoA transferase-like |
| 家族 Family family | c.124.1.5 — IF2B-like |
| 结构域编号 domain_id | d1t5oa2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1t5ob1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.124 — NagB/RpiA/CoA transferase-like |
| 超家族 Superfamily superfamily | c.124.1 — NagB/RpiA/CoA transferase-like |
| 家族 Family family | c.124.1.5 — IF2B-like |
| 结构域编号 domain_id | d1t5ob2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1t5oc1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.124 — NagB/RpiA/CoA transferase-like |
| 超家族 Superfamily superfamily | c.124.1 — NagB/RpiA/CoA transferase-like |
| 家族 Family family | c.124.1.5 — IF2B-like |
| 结构域编号 domain_id | d1t5oc2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1t5od1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.124 — NagB/RpiA/CoA transferase-like |
| 超家族 Superfamily superfamily | c.124.1 — NagB/RpiA/CoA transferase-like |
| 家族 Family family | c.124.1.5 — IF2B-like |
| 结构域编号 domain_id | d1t5od2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1t5oA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 420 — translation initiation factor eif-2b, domain 1 |
| 结构域编号 domain_id | 1t5oA02 |
| 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 | 10470 — Translation initiation factor eif-2b; domain 2 |
| 结构域编号 domain_id | 1t5oB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 420 — translation initiation factor eif-2b, domain 1 |
| 结构域编号 domain_id | 1t5oB02 |
| 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 | 10470 — Translation initiation factor eif-2b; domain 2 |
| 结构域编号 domain_id | 1t5oC01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 420 — translation initiation factor eif-2b, domain 1 |
| 结构域编号 domain_id | 1t5oC02 |
| 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 | 10470 — Translation initiation factor eif-2b; domain 2 |
| 结构域编号 domain_id | 1t5oD01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 420 — translation initiation factor eif-2b, domain 1 |
| 结构域编号 domain_id | 1t5oD02 |
| 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 | 10470 — Translation initiation factor eif-2b; domain 2 |