1mjg
;CRYSTAL STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE(CODH/ACS) FROM MOORELLA THERMOACETICA (F. CLOSTRIDIUM THERMOACETICUM) ;
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 | 1mjg |
| 沉积日期 deposition_date | 2002-08-27 |
| 结构标题 title | ;CRYSTAL STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE(CODH/ACS) FROM MOORELLA THERMOACETICA (F. CLOSTRIDIUM THERMOACETICUM) ; |
| 关键词 keywords | ;Carbon monoxide dehydrogenase(CODH), Acetyl-CoA Synthase (ACS), Nickel-Iron-Sulfur cluster (Ni-Fe-S), Nickel-Coopper-Iron-Sulfur (Ni-Cu-Fe-S) Cluster, Hydrophobic CO channel, substrate tunnel, Helical domain, Rossmann fold, Electron transfer, Clostridium thermoaceticum, Wood-Ljundahl pathway, 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 | 66.45 Å |
| 回转半径 Rg (电子) rg_electron | 66.59 Å |
| 零角强度 I(0) i0 | 5445770000.00 |
| 分子量 molecular_weight | 622550.0 kDa |
| 排除体积 excluded_volume | 777530 ų |
| 包络体积 envelope_volume | 1074700 ų |
| 水化壳体积 shell_volume | 132700 ų |
| 包络直径 envelope_diameter | 234.4 Å |
| 壳层 Rg shell_rg | 67.29 Å |
| 包络 Rg envelope_rg | 65.86 Å |
| 形状 Rg shape_rg | 66.65 Å |
| 总 Rg total_rg | 66.40 Å |
| 总原子数 total_atoms | 43424 |
| 残基数 n_residues | 5600 |
| 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 | 233.2 Å |
| Rg (实空间) rg_real | 66.47 Å |
| Rg 误差 (实空间) rg_real_error | 2.17 Å |
| I(0) (实空间) i0_real | 5.4460e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.0980e+08 |
| Rg (倒空间) rg_reciprocal | 66.38 Å |
| I(0) (倒空间) i0_reciprocal | 5445000000.0000 |
| 解质量估计 total_estimate | 0.8730 |
| 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 | 87.4 Å |
| 偏度 Skewness skewness | 0.259 |
| 峰度 Kurtosis kurtosis | -0.456 |
| 角度范围 angular_range | — – 0.1200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0004 |
| 最高正则化参数 α highest_alpha | 274900000.0000 |
| 实空间数据点数 n_real_points | 25 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.834 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (8)
6. 折叠分类 (SCOP + CATH) 40 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d1mjga_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.26 — Prismane protein-like |
| 超家族 Superfamily superfamily | e.26.1 — Prismane protein-like |
| 家族 Family family | e.26.1.2 — Carbon monoxide dehydrogenase |
| 结构域编号 domain_id | d1mjgb_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.26 — Prismane protein-like |
| 超家族 Superfamily superfamily | e.26.1 — Prismane protein-like |
| 家族 Family family | e.26.1.2 — Carbon monoxide dehydrogenase |
| 结构域编号 domain_id | d1mjgc_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.26 — Prismane protein-like |
| 超家族 Superfamily superfamily | e.26.1 — Prismane protein-like |
| 家族 Family family | e.26.1.2 — Carbon monoxide dehydrogenase |
| 结构域编号 domain_id | d1mjgd_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.26 — Prismane protein-like |
| 超家族 Superfamily superfamily | e.26.1 — Prismane protein-like |
| 家族 Family family | e.26.1.2 — Carbon monoxide dehydrogenase |
| 结构域编号 domain_id | d1mjgm_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.26 — Prismane protein-like |
| 超家族 Superfamily superfamily | e.26.1 — Prismane protein-like |
| 家族 Family family | e.26.1.3 — Acetyl-CoA synthase |
| 结构域编号 domain_id | d1mjgn_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.26 — Prismane protein-like |
| 超家族 Superfamily superfamily | e.26.1 — Prismane protein-like |
| 家族 Family family | e.26.1.3 — Acetyl-CoA synthase |
| 结构域编号 domain_id | d1mjgo_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.26 — Prismane protein-like |
| 超家族 Superfamily superfamily | e.26.1 — Prismane protein-like |
| 家族 Family family | e.26.1.3 — Acetyl-CoA synthase |
| 结构域编号 domain_id | d1mjgp_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.26 — Prismane protein-like |
| 超家族 Superfamily superfamily | e.26.1 — Prismane protein-like |
| 家族 Family family | e.26.1.3 — Acetyl-CoA synthase |
CATH v4.4 (32 domains)
| 结构域编号 domain_id | 1mjgA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1mjgB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1mjgC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgC03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1mjgD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgD03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1mjgM01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 |
| 结构域编号 domain_id | 1mjgM02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgM03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 |
| 结构域编号 domain_id | 1mjgM04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 970 — Ribonuclease HI; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 |
| 结构域编号 domain_id | 1mjgM05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 |
| 结构域编号 domain_id | 1mjgN01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 |
| 结构域编号 domain_id | 1mjgN02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgN03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 |
| 结构域编号 domain_id | 1mjgN04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 970 — Ribonuclease HI; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 |
| 结构域编号 domain_id | 1mjgN05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 |
| 结构域编号 domain_id | 1mjgO01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 |
| 结构域编号 domain_id | 1mjgO02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgO03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 |
| 结构域编号 domain_id | 1mjgO04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 970 — Ribonuclease HI; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 |
| 结构域编号 domain_id | 1mjgO05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 |
| 结构域编号 domain_id | 1mjgP01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 190 — Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 |
| 结构域编号 domain_id | 1mjgP02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 2030 — |
| 结构域编号 domain_id | 1mjgP03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1650 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 |
| 结构域编号 domain_id | 1mjgP04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 970 — Ribonuclease HI; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 |
| 结构域编号 domain_id | 1mjgP05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1470 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 |