2gsm
Catalytic Core (Subunits I and II) of Cytochrome c oxidase from Rhodobacter sphaeroides
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 | 2gsm |
| 沉积日期 deposition_date | 2006-04-26 |
| 结构标题 title | Catalytic Core (Subunits I and II) of Cytochrome c oxidase from Rhodobacter sphaeroides |
| 关键词 keywords | transmembrane protein complex, 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 | 47.52 Å |
| 回转半径 Rg (电子) rg_electron | 47.70 Å |
| 零角强度 I(0) i0 | 409089000.00 |
| 分子量 molecular_weight | 186490.0 kDa |
| 排除体积 excluded_volume | 239820 ų |
| 包络体积 envelope_volume | 298080 ų |
| 水化壳体积 shell_volume | 51268 ų |
| 包络直径 envelope_diameter | 163.3 Å |
| 壳层 Rg shell_rg | 52.76 Å |
| 包络 Rg envelope_rg | 46.90 Å |
| 形状 Rg shape_rg | 47.69 Å |
| 总 Rg total_rg | 47.94 Å |
| 总原子数 total_atoms | 13141 |
| 残基数 n_residues | 1581 |
| 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 | 159.2 Å |
| Rg (实空间) rg_real | 47.85 Å |
| Rg 误差 (实空间) rg_real_error | 1.87 Å |
| I(0) (实空间) i0_real | 4.0910e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.0880e+06 |
| Rg (倒空间) rg_reciprocal | 47.53 Å |
| I(0) (倒空间) i0_reciprocal | 408900000.0000 |
| 解质量估计 total_estimate | 0.8024 |
| 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 | 33.8 Å |
| 偏度 Skewness skewness | 0.292 |
| 峰度 Kurtosis kurtosis | -0.874 |
| 角度范围 angular_range | — – 0.1650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 49740000.0000 |
| 实空间数据点数 n_real_points | 34 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.645; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.728; Smooth: 0.763 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (11)
6. 折叠分类 (SCOP + CATH) 14 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d2gsma_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.24 — Cytochrome c oxidase subunit I-like |
| 超家族 Superfamily superfamily | f.24.1 — Cytochrome c oxidase subunit I-like |
| 家族 Family family | f.24.1.1 — Cytochrome c oxidase subunit I-like |
| 结构域编号 domain_id | d2gsmb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.6 — Cupredoxin-like |
| 超家族 Superfamily superfamily | b.6.1 — Cupredoxins |
| 家族 Family family | b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II |
| 结构域编号 domain_id | d2gsmb2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.17 — Transmembrane helix hairpin |
| 超家族 Superfamily superfamily | f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region |
| 家族 Family family | f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region |
| 结构域编号 domain_id | d2gsmb3 |
| 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 | d2gsmc_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.24 — Cytochrome c oxidase subunit I-like |
| 超家族 Superfamily superfamily | f.24.1 — Cytochrome c oxidase subunit I-like |
| 家族 Family family | f.24.1.1 — Cytochrome c oxidase subunit I-like |
| 结构域编号 domain_id | d2gsmd1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.6 — Cupredoxin-like |
| 超家族 Superfamily superfamily | b.6.1 — Cupredoxins |
| 家族 Family family | b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II |
| 结构域编号 domain_id | d2gsmd2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.17 — Transmembrane helix hairpin |
| 超家族 Superfamily superfamily | f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region |
| 家族 Family family | f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region |
| 结构域编号 domain_id | d2gsmd3 |
| 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 (6 domains)
| 结构域编号 domain_id | 2gsmA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 210 — Cytochrome C Oxidase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome c oxidase-like, subunit I domain |
| 结构域编号 domain_id | 2gsmB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 90 — |
| 结构域编号 domain_id | 2gsmB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 420 — Cupredoxins - blue copper proteins |
| 结构域编号 domain_id | 2gsmC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 210 — Cytochrome C Oxidase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome c oxidase-like, subunit I domain |
| 结构域编号 domain_id | 2gsmD01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 90 — |
| 结构域编号 domain_id | 2gsmD02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 420 — Cupredoxins - blue copper proteins |