1q0d
Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state
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 | 1q0d |
| 沉积日期 deposition_date | 2003-07-16 |
| 结构标题 title | Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state |
| 关键词 keywords | HOMOHEXAMER OF FOUR-HELIX BUNDLES, OXIDOREDUCTASE; 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 | 41.69 Å |
| 回转半径 Rg (电子) rg_electron | 41.84 Å |
| 零角强度 I(0) i0 | 390261000.00 |
| 分子量 molecular_weight | 160450.0 kDa |
| 排除体积 excluded_volume | 199720 ų |
| 包络体积 envelope_volume | 253180 ų |
| 水化壳体积 shell_volume | 50927 ų |
| 包络直径 envelope_diameter | 139.7 Å |
| 壳层 Rg shell_rg | 46.30 Å |
| 包络 Rg envelope_rg | 41.27 Å |
| 形状 Rg shape_rg | 41.87 Å |
| 总 Rg total_rg | 41.95 Å |
| 总原子数 total_atoms | 11264 |
| 残基数 n_residues | 1404 |
| 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 | 144.5 Å |
| Rg (实空间) rg_real | 41.90 Å |
| Rg 误差 (实空间) rg_real_error | 1.50 Å |
| I(0) (实空间) i0_real | 3.9030e+08 |
| I(0) 误差 (实空间) i0_real_error | 6.6110e+06 |
| Rg (倒空间) rg_reciprocal | 41.69 Å |
| I(0) (倒空间) i0_reciprocal | 390200000.0000 |
| 解质量估计 total_estimate | 0.7126 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 4 |
| 主峰位置 r_peak_primary | 34.2 Å |
| 偏度 Skewness skewness | 0.390 |
| 峰度 Kurtosis kurtosis | -0.756 |
| 角度范围 angular_range | — – 0.1900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 386000000.0000 |
| 实空间数据点数 n_real_points | 39 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.471; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 24 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1q0da_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0db_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0dc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0dd_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0de_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0df_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0dg_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0dh_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0di_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0dj_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0dk_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
| 结构域编号 domain_id | d1q0dl_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.22 — Nickel-containing superoxide dismutase, NiSOD |
| 家族 Family family | a.24.22.1 — Nickel-containing superoxide dismutase, NiSOD |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1q0dA00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dB00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dC00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dD00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dE00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dF00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dG00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dH00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dI00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dJ00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dK00 |
| 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 | 400 — Nickel-containing superoxide dismutase |
| 结构域编号 domain_id | 1q0dL00 |
| 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 | 400 — Nickel-containing superoxide dismutase |