1hbu
METHYL-COENZYME M REDUCTASE IN THE MCR-RED1-SILENT STATE IN COMPLEX with COENZYME M
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 | 1hbu |
| 沉积日期 deposition_date | 2001-04-20 |
| 结构标题 title | METHYL-COENZYME M REDUCTASE IN THE MCR-RED1-SILENT STATE IN COMPLEX with COENZYME M |
| 关键词 keywords | METHANOGENESIS, BIOLOGICAL METHANOGENESIS, NI-ENZYME, OXIDOREDUCTASE; METHANOGENESIS |
| 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 | 38.25 Å |
| 回转半径 Rg (电子) rg_electron | 37.39 Å |
| 零角强度 I(0) i0 | 1151670000.00 |
| 分子量 molecular_weight | 276120.0 kDa |
| 排除体积 excluded_volume | 343590 ų |
| 包络体积 envelope_volume | 385640 ų |
| 水化壳体积 shell_volume | 79210 ų |
| 包络直径 envelope_diameter | 127.3 Å |
| 壳层 Rg shell_rg | 47.46 Å |
| 包络 Rg envelope_rg | 37.84 Å |
| 形状 Rg shape_rg | 37.40 Å |
| 总 Rg total_rg | 37.81 Å |
| 总原子数 total_atoms | 19385 |
| 残基数 n_residues | 2464 |
| 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 | 132.8 Å |
| Rg (实空间) rg_real | 38.07 Å |
| Rg 误差 (实空间) rg_real_error | 1.21 Å |
| I(0) (实空间) i0_real | 1.1520e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.0560e+07 |
| Rg (倒空间) rg_reciprocal | 38.18 Å |
| I(0) (倒空间) i0_reciprocal | 1152000000.0000 |
| 解质量估计 total_estimate | 0.7810 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 48.6 Å |
| 偏度 Skewness skewness | 0.261 |
| 峰度 Kurtosis kurtosis | -0.337 |
| 角度范围 angular_range | — – 0.2050 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 538000000.0000 |
| 实空间数据点数 n_real_points | 42 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.722; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (12)
6. 折叠分类 (SCOP + CATH) 22 domains
SCOP 2.08 (10 domains)
| 结构域编号 domain_id | d1hbua1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 超家族 Superfamily superfamily | a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 家族 Family family | a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 结构域编号 domain_id | d1hbua2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.31 — Methyl-coenzyme M reductase subunits |
| 家族 Family family | d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain |
| 结构域编号 domain_id | d1hbub1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 超家族 Superfamily superfamily | a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 家族 Family family | a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 结构域编号 domain_id | d1hbub2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.31 — Methyl-coenzyme M reductase subunits |
| 家族 Family family | d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain |
| 结构域编号 domain_id | d1hbuc_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.31 — Methyl-coenzyme M reductase subunits |
| 家族 Family family | d.58.31.1 — Methyl-coenzyme M reductase gamma chain |
| 结构域编号 domain_id | d1hbud1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 超家族 Superfamily superfamily | a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 家族 Family family | a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 结构域编号 domain_id | d1hbud2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.31 — Methyl-coenzyme M reductase subunits |
| 家族 Family family | d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain |
| 结构域编号 domain_id | d1hbue1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.89 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 超家族 Superfamily superfamily | a.89.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 家族 Family family | a.89.1.1 — Methyl-coenzyme M reductase alpha and beta chain C-terminal domain |
| 结构域编号 domain_id | d1hbue2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.31 — Methyl-coenzyme M reductase subunits |
| 家族 Family family | d.58.31.2 — Methyl-coenzyme M reductase alpha and beta chain N-terminal domain |
| 结构域编号 domain_id | d1hbuf_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.31 — Methyl-coenzyme M reductase subunits |
| 家族 Family family | d.58.31.1 — Methyl-coenzyme M reductase gamma chain |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1hbuA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 390 — Methyl-coenzyme M Reductase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methyl-coenzyme M Reductase; Chain A, domain 1 |
| 结构域编号 domain_id | 1hbuA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 470 — |
| 结构域编号 domain_id | 1hbuA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 840 — Methyl-coenzyme M Reductase; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal |
| 结构域编号 domain_id | 1hbuB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 470 — |
| 结构域编号 domain_id | 1hbuB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 840 — Methyl-coenzyme M Reductase; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal |
| 结构域编号 domain_id | 1hbuC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 320 — Lambda Exonuclease; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Methyl-coenzyme M reductase, gamma subunit |
| 结构域编号 domain_id | 1hbuD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 390 — Methyl-coenzyme M Reductase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methyl-coenzyme M Reductase; Chain A, domain 1 |
| 结构域编号 domain_id | 1hbuD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 470 — |
| 结构域编号 domain_id | 1hbuD03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 840 — Methyl-coenzyme M Reductase; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal |
| 结构域编号 domain_id | 1hbuE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 470 — |
| 结构域编号 domain_id | 1hbuE02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 840 — Methyl-coenzyme M Reductase; Chain B, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal |
| 结构域编号 domain_id | 1hbuF00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 320 — Lambda Exonuclease; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Methyl-coenzyme M reductase, gamma subunit |