1q3s
Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)
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 | 1q3s |
| 沉积日期 deposition_date | 2003-07-31 |
| 结构标题 title | Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP) |
| 关键词 keywords | chaperone, chaperonin, thermosome; CHAPERONE |
| 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 | 56.85 Å |
| 回转半径 Rg (电子) rg_electron | 56.26 Å |
| 零角强度 I(0) i0 | 2831240000.00 |
| 分子量 molecular_weight | 453550.0 kDa |
| 排除体积 excluded_volume | 572070 ų |
| 包络体积 envelope_volume | 878780 ų |
| 水化壳体积 shell_volume | 128950 ų |
| 包络直径 envelope_diameter | 160.8 Å |
| 壳层 Rg shell_rg | 64.14 Å |
| 包络 Rg envelope_rg | 51.59 Å |
| 形状 Rg shape_rg | 56.29 Å |
| 总 Rg total_rg | 56.37 Å |
| 总原子数 total_atoms | 31751 |
| 残基数 n_residues | 4136 |
| 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 | 162.9 Å |
| Rg (实空间) rg_real | 56.42 Å |
| Rg 误差 (实空间) rg_real_error | 1.15 Å |
| I(0) (实空间) i0_real | 2.8310e+09 |
| I(0) 误差 (实空间) i0_real_error | 5.4180e+07 |
| Rg (倒空间) rg_reciprocal | 57.19 Å |
| I(0) (倒空间) i0_reciprocal | 2834000000.0000 |
| 解质量估计 total_estimate | 0.8532 |
| 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 | 87.3 Å |
| 偏度 Skewness skewness | -0.137 |
| 峰度 Kurtosis kurtosis | -0.726 |
| 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 | 145800000.0000 |
| 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: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.263 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 48 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1q3sa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.129 — GroEL equatorial domain-like |
| 超家族 Superfamily superfamily | a.129.1 — GroEL equatorial domain-like |
| 家族 Family family | a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain |
| 结构域编号 domain_id | d1q3sa2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.5 — GroEL apical domain-like |
| 家族 Family family | c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain |
| 结构域编号 domain_id | d1q3sa3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.56 — GroEL-intermediate domain like |
| 超家族 Superfamily superfamily | d.56.1 — GroEL-intermediate domain like |
| 家族 Family family | d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain |
| 结构域编号 domain_id | d1q3sb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.129 — GroEL equatorial domain-like |
| 超家族 Superfamily superfamily | a.129.1 — GroEL equatorial domain-like |
| 家族 Family family | a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain |
| 结构域编号 domain_id | d1q3sb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.5 — GroEL apical domain-like |
| 家族 Family family | c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain |
| 结构域编号 domain_id | d1q3sb3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.56 — GroEL-intermediate domain like |
| 超家族 Superfamily superfamily | d.56.1 — GroEL-intermediate domain like |
| 家族 Family family | d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain |
| 结构域编号 domain_id | d1q3sc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.129 — GroEL equatorial domain-like |
| 超家族 Superfamily superfamily | a.129.1 — GroEL equatorial domain-like |
| 家族 Family family | a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain |
| 结构域编号 domain_id | d1q3sc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.5 — GroEL apical domain-like |
| 家族 Family family | c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain |
| 结构域编号 domain_id | d1q3sc3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.56 — GroEL-intermediate domain like |
| 超家族 Superfamily superfamily | d.56.1 — GroEL-intermediate domain like |
| 家族 Family family | d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain |
| 结构域编号 domain_id | d1q3sd1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.129 — GroEL equatorial domain-like |
| 超家族 Superfamily superfamily | a.129.1 — GroEL equatorial domain-like |
| 家族 Family family | a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain |
| 结构域编号 domain_id | d1q3sd2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.5 — GroEL apical domain-like |
| 家族 Family family | c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain |
| 结构域编号 domain_id | d1q3sd3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.56 — GroEL-intermediate domain like |
| 超家族 Superfamily superfamily | d.56.1 — GroEL-intermediate domain like |
| 家族 Family family | d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain |
| 结构域编号 domain_id | d1q3se1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.129 — GroEL equatorial domain-like |
| 超家族 Superfamily superfamily | a.129.1 — GroEL equatorial domain-like |
| 家族 Family family | a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain |
| 结构域编号 domain_id | d1q3se2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.5 — GroEL apical domain-like |
| 家族 Family family | c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain |
| 结构域编号 domain_id | d1q3se3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.56 — GroEL-intermediate domain like |
| 超家族 Superfamily superfamily | d.56.1 — GroEL-intermediate domain like |
| 家族 Family family | d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain |
| 结构域编号 domain_id | d1q3sf1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.129 — GroEL equatorial domain-like |
| 超家族 Superfamily superfamily | a.129.1 — GroEL equatorial domain-like |
| 家族 Family family | a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain |
| 结构域编号 domain_id | d1q3sf2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.5 — GroEL apical domain-like |
| 家族 Family family | c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain |
| 结构域编号 domain_id | d1q3sf3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.56 — GroEL-intermediate domain like |
| 超家族 Superfamily superfamily | d.56.1 — GroEL-intermediate domain like |
| 家族 Family family | d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain |
| 结构域编号 domain_id | d1q3sg1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.129 — GroEL equatorial domain-like |
| 超家族 Superfamily superfamily | a.129.1 — GroEL equatorial domain-like |
| 家族 Family family | a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain |
| 结构域编号 domain_id | d1q3sg2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.5 — GroEL apical domain-like |
| 家族 Family family | c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain |
| 结构域编号 domain_id | d1q3sg3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.56 — GroEL-intermediate domain like |
| 超家族 Superfamily superfamily | d.56.1 — GroEL-intermediate domain like |
| 家族 Family family | d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain |
| 结构域编号 domain_id | d1q3sh1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.129 — GroEL equatorial domain-like |
| 超家族 Superfamily superfamily | a.129.1 — GroEL equatorial domain-like |
| 家族 Family family | a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain |
| 结构域编号 domain_id | d1q3sh2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.5 — GroEL apical domain-like |
| 家族 Family family | c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain |
| 结构域编号 domain_id | d1q3sh3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.56 — GroEL-intermediate domain like |
| 超家族 Superfamily superfamily | d.56.1 — GroEL-intermediate domain like |
| 家族 Family family | d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 1q3sA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 560 — GROEL; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL-like equatorial domain |
| 结构域编号 domain_id | 1q3sA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 260 — GROEL; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — TCP-1-like chaperonin intermediate domain |
| 结构域编号 domain_id | 1q3sA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 7 — GroEL |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL |
| 结构域编号 domain_id | 1q3sB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 560 — GROEL; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL-like equatorial domain |
| 结构域编号 domain_id | 1q3sB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 260 — GROEL; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — TCP-1-like chaperonin intermediate domain |
| 结构域编号 domain_id | 1q3sB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 7 — GroEL |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL |
| 结构域编号 domain_id | 1q3sC01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 560 — GROEL; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL-like equatorial domain |
| 结构域编号 domain_id | 1q3sC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 260 — GROEL; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — TCP-1-like chaperonin intermediate domain |
| 结构域编号 domain_id | 1q3sC03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 7 — GroEL |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL |
| 结构域编号 domain_id | 1q3sD01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 560 — GROEL; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL-like equatorial domain |
| 结构域编号 domain_id | 1q3sD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 260 — GROEL; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — TCP-1-like chaperonin intermediate domain |
| 结构域编号 domain_id | 1q3sD03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 7 — GroEL |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL |
| 结构域编号 domain_id | 1q3sE01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 560 — GROEL; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL-like equatorial domain |
| 结构域编号 domain_id | 1q3sE02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 260 — GROEL; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — TCP-1-like chaperonin intermediate domain |
| 结构域编号 domain_id | 1q3sE03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 7 — GroEL |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL |
| 结构域编号 domain_id | 1q3sF01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 560 — GROEL; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL-like equatorial domain |
| 结构域编号 domain_id | 1q3sF02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 260 — GROEL; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — TCP-1-like chaperonin intermediate domain |
| 结构域编号 domain_id | 1q3sF03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 7 — GroEL |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL |
| 结构域编号 domain_id | 1q3sG01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 560 — GROEL; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL-like equatorial domain |
| 结构域编号 domain_id | 1q3sG02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 260 — GROEL; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — TCP-1-like chaperonin intermediate domain |
| 结构域编号 domain_id | 1q3sG03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 7 — GroEL |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL |
| 结构域编号 domain_id | 1q3sH01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 560 — GROEL; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL-like equatorial domain |
| 结构域编号 domain_id | 1q3sH02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 260 — GROEL; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — TCP-1-like chaperonin intermediate domain |
| 结构域编号 domain_id | 1q3sH03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 7 — GroEL |
| 同源超家族 H-superfamily homologous superfamily | 10 — GroEL |