1w3s
The crystal structure of RecO from Deinococcus radiodurans.
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 | 1w3s |
| 沉积日期 deposition_date | 2004-07-18 |
| 结构标题 title | The crystal structure of RecO from Deinococcus radiodurans. |
| 关键词 keywords | DNA REPAIR, SAD, CYS4 ZINC FINGER, OB-FOLD, RECO; DNA REPAIR |
| 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 | 26.33 Å |
| 回转半径 Rg (电子) rg_electron | 25.01 Å |
| 零角强度 I(0) i0 | 41446000.00 |
| 分子量 molecular_weight | 50146.0 kDa |
| 排除体积 excluded_volume | 63022 ų |
| 包络体积 envelope_volume | 78738 ų |
| 水化壳体积 shell_volume | 26617 ų |
| 包络直径 envelope_diameter | 87.9 Å |
| 壳层 Rg shell_rg | 31.73 Å |
| 包络 Rg envelope_rg | 25.09 Å |
| 形状 Rg shape_rg | 24.91 Å |
| 总 Rg total_rg | 26.10 Å |
| 总原子数 total_atoms | 3534 |
| 残基数 n_residues | 461 |
| 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 | 84.2 Å |
| Rg (实空间) rg_real | 26.27 Å |
| Rg 误差 (实空间) rg_real_error | 0.62 Å |
| I(0) (实空间) i0_real | 4.1450e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.9170e+05 |
| Rg (倒空间) rg_reciprocal | 26.29 Å |
| I(0) (倒空间) i0_reciprocal | 41450000.0000 |
| 解质量估计 total_estimate | 0.9068 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 29.5 Å |
| 偏度 Skewness skewness | 0.241 |
| 峰度 Kurtosis kurtosis | -0.484 |
| 角度范围 angular_range | — – 0.3000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 7215000.0000 |
| 实空间数据点数 n_real_points | 61 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.988 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1w3sa1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.13 — RecO N-terminal domain-like |
| 结构域编号 domain_id | d1w3sa2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.45 — ArfGap/RecO-like zinc finger |
| 超家族 Superfamily superfamily | g.45.1 — ArfGap/RecO-like zinc finger |
| 家族 Family family | g.45.1.2 — RecO C-terminal domain-like |
| 结构域编号 domain_id | d1w3sb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.13 — RecO N-terminal domain-like |
| 结构域编号 domain_id | d1w3sb2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.45 — ArfGap/RecO-like zinc finger |
| 超家族 Superfamily superfamily | g.45.1 — ArfGap/RecO-like zinc finger |
| 家族 Family family | g.45.1.2 — RecO C-terminal domain-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1w3sA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 1w3sA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1440 — de novo design (two linked rop proteins) |
| 同源超家族 H-superfamily homologous superfamily | 120 — Recombination protein O, C-terminal domain |
| 结构域编号 domain_id | 1w3sA03 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 20 — Other non-globular |
| 拓扑 Topology topology | 220 — Erythroid Transcription Factor GATA-1; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Recombination protein O, zinc-binding domain |
| 结构域编号 domain_id | 1w3sB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 1w3sB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1440 — de novo design (two linked rop proteins) |
| 同源超家族 H-superfamily homologous superfamily | 120 — Recombination protein O, C-terminal domain |
| 结构域编号 domain_id | 1w3sB03 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 20 — Other non-globular |
| 拓扑 Topology topology | 220 — Erythroid Transcription Factor GATA-1; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Recombination protein O, zinc-binding domain |