1k47
Crystal Structure of the Streptococcus pneumoniae Phosphomevalonate Kinase (PMK)
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 | 1k47 |
| 沉积日期 deposition_date | 2001-10-05 |
| 结构标题 title | Crystal Structure of the Streptococcus pneumoniae Phosphomevalonate Kinase (PMK) |
| 关键词 keywords | ;Alpha/beta single domain belonging to the GHMP kinase superfamily, MvaK2, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, TRANSFERASE ;; TRANSFERASE |
| 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 | 38.74 Å |
| 回转半径 Rg (电子) rg_electron | 37.75 Å |
| 零角强度 I(0) i0 | 677217000.00 |
| 分子量 molecular_weight | 215710.0 kDa |
| 排除体积 excluded_volume | 270670 ų |
| 包络体积 envelope_volume | 354280 ų |
| 水化壳体积 shell_volume | 74422 ų |
| 包络直径 envelope_diameter | 112.0 Å |
| 壳层 Rg shell_rg | 47.09 Å |
| 包络 Rg envelope_rg | 36.61 Å |
| 形状 Rg shape_rg | 37.84 Å |
| 总 Rg total_rg | 38.00 Å |
| 总原子数 total_atoms | 15000 |
| 残基数 n_residues | 1884 |
| 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 | 113.5 Å |
| Rg (实空间) rg_real | 38.33 Å |
| Rg 误差 (实空间) rg_real_error | 0.60 Å |
| I(0) (实空间) i0_real | 6.7720e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1320e+07 |
| Rg (倒空间) rg_reciprocal | 38.59 Å |
| I(0) (倒空间) i0_reciprocal | 677400000.0000 |
| 解质量估计 total_estimate | 0.8979 |
| 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 | 52.6 Å |
| 偏度 Skewness skewness | -0.046 |
| 峰度 Kurtosis kurtosis | -0.555 |
| 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 | 119200000.0000 |
| 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: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.941 |
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) 30 domains
SCOP 2.08 (18 domains)
| 结构域编号 domain_id | d1k47a1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.5 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | d1k47a2 |
| 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.58.26 — GHMP Kinase, C-terminal domain |
| 家族 Family family | d.58.26.4 — Phosphomevalonate kinase (PMK) |
| 结构域编号 domain_id | d1k47a3 |
| 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 | d1k47b1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.5 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | d1k47b2 |
| 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.58.26 — GHMP Kinase, C-terminal domain |
| 家族 Family family | d.58.26.4 — Phosphomevalonate kinase (PMK) |
| 结构域编号 domain_id | d1k47b3 |
| 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 | d1k47c1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.5 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | d1k47c2 |
| 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.58.26 — GHMP Kinase, C-terminal domain |
| 家族 Family family | d.58.26.4 — Phosphomevalonate kinase (PMK) |
| 结构域编号 domain_id | d1k47c3 |
| 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 | d1k47d1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.5 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | d1k47d2 |
| 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.58.26 — GHMP Kinase, C-terminal domain |
| 家族 Family family | d.58.26.4 — Phosphomevalonate kinase (PMK) |
| 结构域编号 domain_id | d1k47d3 |
| 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 | d1k47e1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.5 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | d1k47e2 |
| 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.58.26 — GHMP Kinase, C-terminal domain |
| 家族 Family family | d.58.26.4 — Phosphomevalonate kinase (PMK) |
| 结构域编号 domain_id | d1k47e3 |
| 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 | d1k47f1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.14 — Ribosomal protein S5 domain 2-like |
| 超家族 Superfamily superfamily | d.14.1 — Ribosomal protein S5 domain 2-like |
| 家族 Family family | d.14.1.5 — GHMP Kinase, N-terminal domain |
| 结构域编号 domain_id | d1k47f2 |
| 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.58.26 — GHMP Kinase, C-terminal domain |
| 家族 Family family | d.58.26.4 — Phosphomevalonate kinase (PMK) |
| 结构域编号 domain_id | d1k47f3 |
| 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 (12 domains)
| 结构域编号 domain_id | 1k47A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1k47A02 |
| 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 | 890 — GHMP kinase, C-terminal domain |
| 结构域编号 domain_id | 1k47B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1k47B02 |
| 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 | 890 — GHMP kinase, C-terminal domain |
| 结构域编号 domain_id | 1k47C01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1k47C02 |
| 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 | 890 — GHMP kinase, C-terminal domain |
| 结构域编号 domain_id | 1k47D01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1k47D02 |
| 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 | 890 — GHMP kinase, C-terminal domain |
| 结构域编号 domain_id | 1k47E01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1k47E02 |
| 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 | 890 — GHMP kinase, C-terminal domain |
| 结构域编号 domain_id | 1k47F01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 230 — Ribosomal Protein S5; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1k47F02 |
| 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 | 890 — GHMP kinase, C-terminal domain |