2af7
;Crystal structure of the gamma-carboxymuconolactone decarboxylase from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Consortium target TT747. ;
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 | 2af7 |
| 沉积日期 deposition_date | 2005-07-25 |
| 结构标题 title | ;Crystal structure of the gamma-carboxymuconolactone decarboxylase from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Consortium target TT747. ; |
| 关键词 keywords | ;Gamma-carboxymuconolactone decarboxylase, O26336_METTH, NESG, TT747, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, LYASE ;; LYASE |
| 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 | 36.16 Å |
| 回转半径 Rg (电子) rg_electron | 35.93 Å |
| 零角强度 I(0) i0 | 223469000.00 |
| 分子量 molecular_weight | 118650.0 kDa |
| 排除体积 excluded_volume | 147410 ų |
| 包络体积 envelope_volume | 194480 ų |
| 水化壳体积 shell_volume | 46681 ų |
| 包络直径 envelope_diameter | 138.6 Å |
| 壳层 Rg shell_rg | 40.64 Å |
| 包络 Rg envelope_rg | 36.83 Å |
| 形状 Rg shape_rg | 35.94 Å |
| 总 Rg total_rg | 36.22 Å |
| 总原子数 total_atoms | 8199 |
| 残基数 n_residues | 1035 |
| 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 | 130.7 Å |
| Rg (实空间) rg_real | 36.55 Å |
| Rg 误差 (实空间) rg_real_error | 1.39 Å |
| I(0) (实空间) i0_real | 2.2350e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.5470e+06 |
| Rg (倒空间) rg_reciprocal | 36.31 Å |
| I(0) (倒空间) i0_reciprocal | 223400000.0000 |
| 解质量估计 total_estimate | 0.7950 |
| 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 | 38.6 Å |
| 偏度 Skewness skewness | 0.696 |
| 峰度 Kurtosis kurtosis | 0.179 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 39400000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.598; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.806; Smooth: 0.733 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 18 domains
SCOP 2.08 (9 domains)
| 结构域编号 domain_id | d2af7a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
| 结构域编号 domain_id | d2af7b_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
| 结构域编号 domain_id | d2af7c_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
| 结构域编号 domain_id | d2af7d_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
| 结构域编号 domain_id | d2af7e_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
| 结构域编号 domain_id | d2af7f_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
| 结构域编号 domain_id | d2af7g_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
| 结构域编号 domain_id | d2af7h_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
| 结构域编号 domain_id | d2af7i_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.152 — AhpD-like |
| 超家族 Superfamily superfamily | a.152.1 — AhpD-like |
| 家族 Family family | a.152.1.2 — CMD-like |
CATH v4.4 (9 domains)
| 结构域编号 domain_id | 2af7A00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |
| 结构域编号 domain_id | 2af7B00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |
| 结构域编号 domain_id | 2af7C00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |
| 结构域编号 domain_id | 2af7D00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |
| 结构域编号 domain_id | 2af7E00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |
| 结构域编号 domain_id | 2af7F00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |
| 结构域编号 domain_id | 2af7G00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |
| 结构域编号 domain_id | 2af7H00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |
| 结构域编号 domain_id | 2af7I00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1290 — AhpD-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — AhpD-like |