2dth
;The Crystal Structure of the Orthorhombic Form of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotin and ADP ;
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 | 2dth |
| 沉积日期 deposition_date | 2006-07-12 |
| 结构标题 title | ;The Crystal Structure of the Orthorhombic Form of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotin and ADP ; |
| 关键词 keywords | ;Biotin Biosynthesis, Dimer, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, LIGASE ;; LIGASE |
| 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 | 27.52 Å |
| 回转半径 Rg (电子) rg_electron | 27.14 Å |
| 零角强度 I(0) i0 | 41691500.00 |
| 分子量 molecular_weight | 53110.0 kDa |
| 排除体积 excluded_volume | 67891 ų |
| 包络体积 envelope_volume | 79735 ų |
| 水化壳体积 shell_volume | 26215 ų |
| 包络直径 envelope_diameter | 110.0 Å |
| 壳层 Rg shell_rg | 32.03 Å |
| 包络 Rg envelope_rg | 27.71 Å |
| 形状 Rg shape_rg | 27.13 Å |
| 总 Rg total_rg | 27.68 Å |
| 总原子数 total_atoms | 3740 |
| 残基数 n_residues | 470 |
| 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 | 107.0 Å |
| Rg (实空间) rg_real | 27.90 Å |
| Rg 误差 (实空间) rg_real_error | 1.36 Å |
| I(0) (实空间) i0_real | 4.1690e+07 |
| I(0) 误差 (实空间) i0_real_error | 7.7480e+05 |
| Rg (倒空间) rg_reciprocal | 27.78 Å |
| I(0) (倒空间) i0_reciprocal | 41690000.0000 |
| 解质量估计 total_estimate | 0.7419 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 25.8 Å |
| 偏度 Skewness skewness | 0.692 |
| 峰度 Kurtosis kurtosis | 0.104 |
| 角度范围 angular_range | — – 0.2900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 11150000.0000 |
| 实空间数据点数 n_real_points | 59 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.391; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.527; Smooth: 0.940 |
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) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2dtha1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.1 — Biotin repressor (BirA) |
| 结构域编号 domain_id | d2dtha2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.104 — Class II aaRS and biotin synthetases |
| 超家族 Superfamily superfamily | d.104.1 — Class II aaRS and biotin synthetases |
| 家族 Family family | d.104.1.2 — Biotin holoenzyme synthetase |
| 结构域编号 domain_id | d2dthb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.1 — Biotin repressor (BirA) |
| 结构域编号 domain_id | d2dthb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.104 — Class II aaRS and biotin synthetases |
| 超家族 Superfamily superfamily | d.104.1 — Class II aaRS and biotin synthetases |
| 家族 Family family | d.104.1.2 — Biotin holoenzyme synthetase |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2dthA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 930 — BirA Bifunctional Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bira Bifunctional Protein; Domain 2 |
| 结构域编号 domain_id | 2dthA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 100 — |
| 结构域编号 domain_id | 2dthB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 930 — BirA Bifunctional Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bira Bifunctional Protein; Domain 2 |
| 结构域编号 domain_id | 2dthB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 100 — |