1nkt
CRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEX WITH ADPBS
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 | 1nkt |
| 沉积日期 deposition_date | 2003-01-03 |
| 结构标题 title | CRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEX WITH ADPBS |
| 关键词 keywords | ;PREPROTEIN TRANSLOCATION, ATPASE, TRANSMEMBRANE TRANSPORT, HELICASE-LIKE MOTOR DOMAIN, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, PROTEIN TRANSPORT ;; PROTEIN TRANSPORT |
| 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 | 46.46 Å |
| 回转半径 Rg (电子) rg_electron | 46.31 Å |
| 零角强度 I(0) i0 | 545485000.00 |
| 分子量 molecular_weight | 189350.0 kDa |
| 排除体积 excluded_volume | 235500 ų |
| 包络体积 envelope_volume | 330180 ų |
| 水化壳体积 shell_volume | 58963 ų |
| 包络直径 envelope_diameter | 155.7 Å |
| 壳层 Rg shell_rg | 51.06 Å |
| 包络 Rg envelope_rg | 45.47 Å |
| 形状 Rg shape_rg | 46.34 Å |
| 总 Rg total_rg | 46.38 Å |
| 总原子数 total_atoms | 13316 |
| 残基数 n_residues | 1672 |
| 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 | 155.7 Å |
| Rg (实空间) rg_real | 46.45 Å |
| Rg 误差 (实空间) rg_real_error | 1.45 Å |
| I(0) (实空间) i0_real | 5.4550e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1080e+07 |
| Rg (倒空间) rg_reciprocal | 46.46 Å |
| I(0) (倒空间) i0_reciprocal | 545500000.0000 |
| 解质量估计 total_estimate | 0.6610 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 64.1 Å |
| 偏度 Skewness skewness | 0.202 |
| 峰度 Kurtosis kurtosis | -0.626 |
| 角度范围 angular_range | — – 0.1700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 62760000.0000 |
| 实空间数据点数 n_real_points | 35 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 0.021; Positv: 1.000; Valcen: 0.990; Smooth: 0.864 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 18 domains
SCOP 2.08 (10 domains)
| 结构域编号 domain_id | d1nkta1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.162 — Pre-protein crosslinking domain of SecA |
| 超家族 Superfamily superfamily | a.162.1 — Pre-protein crosslinking domain of SecA |
| 家族 Family family | a.162.1.1 — Pre-protein crosslinking domain of SecA |
| 结构域编号 domain_id | d1nkta2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.172 — Helical scaffold and wing domains of SecA |
| 超家族 Superfamily superfamily | a.172.1 — Helical scaffold and wing domains of SecA |
| 家族 Family family | a.172.1.1 — Helical scaffold and wing domains of SecA |
| 结构域编号 domain_id | d1nkta3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.19 — Tandem AAA-ATPase domain |
| 结构域编号 domain_id | d1nkta4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.19 — Tandem AAA-ATPase domain |
| 结构域编号 domain_id | d1nkta5 |
| 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 | d1nktb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.162 — Pre-protein crosslinking domain of SecA |
| 超家族 Superfamily superfamily | a.162.1 — Pre-protein crosslinking domain of SecA |
| 家族 Family family | a.162.1.1 — Pre-protein crosslinking domain of SecA |
| 结构域编号 domain_id | d1nktb2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.172 — Helical scaffold and wing domains of SecA |
| 超家族 Superfamily superfamily | a.172.1 — Helical scaffold and wing domains of SecA |
| 家族 Family family | a.172.1.1 — Helical scaffold and wing domains of SecA |
| 结构域编号 domain_id | d1nktb3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.19 — Tandem AAA-ATPase domain |
| 结构域编号 domain_id | d1nktb4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.19 — Tandem AAA-ATPase domain |
| 结构域编号 domain_id | d1nktb5 |
| 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 (8 domains)
| 结构域编号 domain_id | 1nktA01 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1nktA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1440 — Pre-protein croslinking domain of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — SecA, preprotein cross-linking domain |
| 结构域编号 domain_id | 1nktA03 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1nktA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3060 — Helical scaffold and wing domains of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — Helical scaffold and wing domains of SecA |
| 结构域编号 domain_id | 1nktB01 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1nktB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1440 — Pre-protein croslinking domain of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — SecA, preprotein cross-linking domain |
| 结构域编号 domain_id | 1nktB03 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1nktB04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3060 — Helical scaffold and wing domains of SecA |
| 同源超家族 H-superfamily homologous superfamily | 10 — Helical scaffold and wing domains of SecA |