1mnm
YEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL STRUCTURE
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 | 1mnm |
| 沉积日期 deposition_date | 1997-11-03 |
| 结构标题 title | YEAST MATALPHA2/MCM1/DNA TERNARY TRANSCRIPTION COMPLEX CRYSTAL STRUCTURE |
| 关键词 keywords | ;TRANSCRIPTION REGULATION, TRANSCRIPTIONAL REPRESSION, DNA-BINDING PROTEIN, COMPLEX (TRANSCRIPTION-HOMEOBOX-DNA), TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/DNA |
| 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 | 27.38 Å |
| 零角强度 I(0) i0 | 62314500.00 |
| 分子量 molecular_weight | 52087.0 kDa |
| 排除体积 excluded_volume | 61016 ų |
| 包络体积 envelope_volume | 82948 ų |
| 水化壳体积 shell_volume | 26566 ų |
| 包络直径 envelope_diameter | 100.7 Å |
| 壳层 Rg shell_rg | 32.94 Å |
| 包络 Rg envelope_rg | 27.81 Å |
| 形状 Rg shape_rg | 27.39 Å |
| 总 Rg total_rg | 27.86 Å |
| 总原子数 total_atoms | 3604 |
| 残基数 n_residues | 372 |
| 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 | 94.8 Å |
| Rg (实空间) rg_real | 27.70 Å |
| Rg 误差 (实空间) rg_real_error | 0.73 Å |
| I(0) (实空间) i0_real | 6.2310e+07 |
| I(0) 误差 (实空间) i0_real_error | 9.8710e+05 |
| Rg (倒空间) rg_reciprocal | 27.65 Å |
| I(0) (倒空间) i0_reciprocal | 62310000.0000 |
| 解质量估计 total_estimate | 0.8649 |
| 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 | 27.8 Å |
| 偏度 Skewness skewness | 0.475 |
| 峰度 Kurtosis kurtosis | -0.263 |
| 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 | 8852000.0000 |
| 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: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.913 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1mnma_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.88 — SRF-like |
| 超家族 Superfamily superfamily | d.88.1 — SRF-like |
| 家族 Family family | d.88.1.1 — SRF-like |
| 结构域编号 domain_id | d1mnmb_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.88 — SRF-like |
| 超家族 Superfamily superfamily | d.88.1 — SRF-like |
| 家族 Family family | d.88.1.1 — SRF-like |
| 结构域编号 domain_id | d1mnmc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.1 — Homeodomain-like |
| 家族 Family family | a.4.1.1 — Homeodomain |
| 结构域编号 domain_id | d1mnmd_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.1 — Homeodomain-like |
| 家族 Family family | a.4.1.1 — Homeodomain |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1mnmA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1810 — SRF-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Transcription factor, MADS-box |
| 结构域编号 domain_id | 1mnmB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1810 — SRF-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Transcription factor, MADS-box |
| 结构域编号 domain_id | 1mnmC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 60 — Homeodomain-like |
| 结构域编号 domain_id | 1mnmD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 60 — Homeodomain-like |