1lnl
Structure of deoxygenated hemocyanin from Rapana thomasiana
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 | 1lnl |
| 沉积日期 deposition_date | 2002-05-03 |
| 结构标题 title | Structure of deoxygenated hemocyanin from Rapana thomasiana |
| 关键词 keywords | hemocyanin, deoxygenated form, oxygen, metal binding site, cooperativity, OXYGEN STORAGE-TRANSPORT COMPLEX; OXYGEN STORAGE/TRANSPORT |
| 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 | 40.34 Å |
| 回转半径 Rg (电子) rg_electron | 39.88 Å |
| 零角强度 I(0) i0 | 309634000.00 |
| 分子量 molecular_weight | 141360.0 kDa |
| 排除体积 excluded_volume | 175130 ų |
| 包络体积 envelope_volume | 237000 ų |
| 水化壳体积 shell_volume | 49256 ų |
| 包络直径 envelope_diameter | 131.3 Å |
| 壳层 Rg shell_rg | 46.02 Å |
| 包络 Rg envelope_rg | 38.78 Å |
| 形状 Rg shape_rg | 39.87 Å |
| 总 Rg total_rg | 40.27 Å |
| 总原子数 total_atoms | 9984 |
| 残基数 n_residues | 1224 |
| 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 | 131.1 Å |
| Rg (实空间) rg_real | 40.32 Å |
| Rg 误差 (实空间) rg_real_error | 1.37 Å |
| I(0) (实空间) i0_real | 3.0960e+08 |
| I(0) 误差 (实空间) i0_real_error | 5.5430e+06 |
| Rg (倒空间) rg_reciprocal | 40.34 Å |
| I(0) (倒空间) i0_reciprocal | 309600000.0000 |
| 解质量估计 total_estimate | 0.8773 |
| 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 | 60.5 Å |
| 偏度 Skewness skewness | 0.174 |
| 峰度 Kurtosis kurtosis | -0.748 |
| 角度范围 angular_range | — – 0.1950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 165700000.0000 |
| 实空间数据点数 n_real_points | 40 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.880 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1lnla1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.86 — Di-copper centre-containing domain |
| 超家族 Superfamily superfamily | a.86.1 — Di-copper centre-containing domain |
| 家族 Family family | a.86.1.1 — Hemocyanin middle domain |
| 结构域编号 domain_id | d1lnla2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.112 — C-terminal domain of mollusc hemocyanin |
| 超家族 Superfamily superfamily | b.112.1 — C-terminal domain of mollusc hemocyanin |
| 家族 Family family | b.112.1.1 — C-terminal domain of mollusc hemocyanin |
| 结构域编号 domain_id | d1lnlb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.86 — Di-copper centre-containing domain |
| 超家族 Superfamily superfamily | a.86.1 — Di-copper centre-containing domain |
| 家族 Family family | a.86.1.1 — Hemocyanin middle domain |
| 结构域编号 domain_id | d1lnlb2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.112 — C-terminal domain of mollusc hemocyanin |
| 超家族 Superfamily superfamily | b.112.1 — C-terminal domain of mollusc hemocyanin |
| 家族 Family family | b.112.1.1 — C-terminal domain of mollusc hemocyanin |
| 结构域编号 domain_id | d1lnlc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.86 — Di-copper centre-containing domain |
| 超家族 Superfamily superfamily | a.86.1 — Di-copper centre-containing domain |
| 家族 Family family | a.86.1.1 — Hemocyanin middle domain |
| 结构域编号 domain_id | d1lnlc2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.112 — C-terminal domain of mollusc hemocyanin |
| 超家族 Superfamily superfamily | b.112.1 — C-terminal domain of mollusc hemocyanin |
| 家族 Family family | b.112.1.1 — C-terminal domain of mollusc hemocyanin |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1lnlA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1280 — di-copper center containing domain from catechol oxidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Di-copper center containing domain from catechol oxidase |
| 结构域编号 domain_id | 1lnlA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 310 — Hemocyanin; Chain: A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Haemocyanin C-terminal domain |
| 结构域编号 domain_id | 1lnlB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1280 — di-copper center containing domain from catechol oxidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Di-copper center containing domain from catechol oxidase |
| 结构域编号 domain_id | 1lnlB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 310 — Hemocyanin; Chain: A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Haemocyanin C-terminal domain |
| 结构域编号 domain_id | 1lnlC01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1280 — di-copper center containing domain from catechol oxidase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Di-copper center containing domain from catechol oxidase |
| 结构域编号 domain_id | 1lnlC02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 310 — Hemocyanin; Chain: A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Haemocyanin C-terminal domain |