1l0v
Quinol-Fumarate Reductase with Menaquinol Molecules
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 | 1l0v |
| 沉积日期 deposition_date | 2002-02-13 |
| 结构标题 title | Quinol-Fumarate Reductase with Menaquinol Molecules |
| 关键词 keywords | fumarate reductase, succinate dehydrogenase, complex II, quinol, membrane protein, 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 | 45.37 Å |
| 回转半径 Rg (电子) rg_electron | 45.44 Å |
| 零角强度 I(0) i0 | 850203000.00 |
| 分子量 molecular_weight | 243630.0 kDa |
| 排除体积 excluded_volume | 305290 ų |
| 包络体积 envelope_volume | 395500 ų |
| 水化壳体积 shell_volume | 70809 ų |
| 包络直径 envelope_diameter | 145.8 Å |
| 壳层 Rg shell_rg | 51.47 Å |
| 包络 Rg envelope_rg | 44.78 Å |
| 形状 Rg shape_rg | 45.52 Å |
| 总 Rg total_rg | 45.42 Å |
| 总原子数 total_atoms | 17046 |
| 残基数 n_residues | 2138 |
| 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 | 144.8 Å |
| Rg (实空间) rg_real | 45.33 Å |
| Rg 误差 (实空间) rg_real_error | 1.03 Å |
| I(0) (实空间) i0_real | 8.5020e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.5420e+07 |
| Rg (倒空间) rg_reciprocal | 45.37 Å |
| I(0) (倒空间) i0_reciprocal | 850200000.0000 |
| 解质量估计 total_estimate | 0.8858 |
| 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 | 45.5 Å |
| 偏度 Skewness skewness | 0.203 |
| 峰度 Kurtosis kurtosis | -0.731 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 121800000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.751 |
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) 30 domains
SCOP 2.08 (14 domains)
| 结构域编号 domain_id | d1l0va1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.7 — Spectrin repeat-like |
| 超家族 Superfamily superfamily | a.7.3 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain |
| 家族 Family family | a.7.3.1 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain |
| 结构域编号 domain_id | d1l0va2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain |
| 结构域编号 domain_id | d1l0va3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain |
| 超家族 Superfamily superfamily | d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain |
| 家族 Family family | d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain |
| 结构域编号 domain_id | d1l0vb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.1 — Globin-like |
| 超家族 Superfamily superfamily | a.1.2 — alpha-helical ferredoxin |
| 家族 Family family | a.1.2.1 — Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain |
| 结构域编号 domain_id | d1l0vb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.4 — 2Fe-2S ferredoxin-like |
| 家族 Family family | d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins |
| 结构域编号 domain_id | d1l0vc_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.21 — Heme-binding four-helical bundle |
| 超家族 Superfamily superfamily | f.21.2 — Fumarate reductase respiratory complex transmembrane subunits |
| 家族 Family family | f.21.2.2 — Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) |
| 结构域编号 domain_id | d1l0vd_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.21 — Heme-binding four-helical bundle |
| 超家族 Superfamily superfamily | f.21.2 — Fumarate reductase respiratory complex transmembrane subunits |
| 家族 Family family | f.21.2.2 — Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) |
| 结构域编号 domain_id | d1l0vm1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.7 — Spectrin repeat-like |
| 超家族 Superfamily superfamily | a.7.3 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain |
| 家族 Family family | a.7.3.1 — Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain |
| 结构域编号 domain_id | d1l0vm2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.4 — Succinate dehydrogenase/fumarate reductase flavoprotein N-terminal domain |
| 结构域编号 domain_id | d1l0vm3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.168 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain |
| 超家族 Superfamily superfamily | d.168.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain |
| 家族 Family family | d.168.1.1 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain |
| 结构域编号 domain_id | d1l0vn1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.1 — Globin-like |
| 超家族 Superfamily superfamily | a.1.2 — alpha-helical ferredoxin |
| 家族 Family family | a.1.2.1 — Fumarate reductase/Succinate dehydogenase iron-sulfur protein, C-terminal domain |
| 结构域编号 domain_id | d1l0vn2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.4 — 2Fe-2S ferredoxin-like |
| 家族 Family family | d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins |
| 结构域编号 domain_id | d1l0vo_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.21 — Heme-binding four-helical bundle |
| 超家族 Superfamily superfamily | f.21.2 — Fumarate reductase respiratory complex transmembrane subunits |
| 家族 Family family | f.21.2.2 — Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) |
| 结构域编号 domain_id | d1l0vp_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.21 — Heme-binding four-helical bundle |
| 超家族 Superfamily superfamily | f.21.2 — Fumarate reductase respiratory complex transmembrane subunits |
| 家族 Family family | f.21.2.2 — Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 1l0vA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1l0vA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 700 — Flavocytochrome C3; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain |
| 结构域编号 domain_id | 1l0vA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 100 — Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain |
| 结构域编号 domain_id | 1l0vA04 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 80 — Rhinovirus 14, subunit 4 |
| 同源超家族 H-superfamily homologous superfamily | 40 — succinate dehydrogenase protein domain |
| 结构域编号 domain_id | 1l0vB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Beta-grasp domain |
| 结构域编号 domain_id | 1l0vB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1060 — Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Alpha-helical ferredoxin |
| 结构域编号 domain_id | 1l0vC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1300 — 3 helical TM bundles of succinate and fumarate reductases |
| 同源超家族 H-superfamily homologous superfamily | 10 — Fumarate reductase/succinate dehydrogenase, transmembrane subunit |
| 结构域编号 domain_id | 1l0vD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1300 — 3 helical TM bundles of succinate and fumarate reductases |
| 同源超家族 H-superfamily homologous superfamily | 10 — Fumarate reductase/succinate dehydrogenase, transmembrane subunit |
| 结构域编号 domain_id | 1l0vM01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1l0vM02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 700 — Flavocytochrome C3; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain |
| 结构域编号 domain_id | 1l0vM03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 100 — Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain |
| 结构域编号 domain_id | 1l0vM04 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 80 — Rhinovirus 14, subunit 4 |
| 同源超家族 H-superfamily homologous superfamily | 40 — succinate dehydrogenase protein domain |
| 结构域编号 domain_id | 1l0vN01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Beta-grasp domain |
| 结构域编号 domain_id | 1l0vN02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1060 — Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Alpha-helical ferredoxin |
| 结构域编号 domain_id | 1l0vO00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1300 — 3 helical TM bundles of succinate and fumarate reductases |
| 同源超家族 H-superfamily homologous superfamily | 10 — Fumarate reductase/succinate dehydrogenase, transmembrane subunit |
| 结构域编号 domain_id | 1l0vP00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1300 — 3 helical TM bundles of succinate and fumarate reductases |
| 同源超家族 H-superfamily homologous superfamily | 10 — Fumarate reductase/succinate dehydrogenase, transmembrane subunit |