1mkm
CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR
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 | 1mkm |
| 沉积日期 deposition_date | 2002-08-29 |
| 结构标题 title | CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR |
| 关键词 keywords | ;STRUCTURAL GENOMICS, WINGED HELIX-TURN-HELIX, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TRANSCRIPTION ;; TRANSCRIPTION |
| 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 | 27.21 Å |
| 回转半径 Rg (电子) rg_electron | 26.13 Å |
| 零角强度 I(0) i0 | 49205600.00 |
| 分子量 molecular_weight | 56557.0 kDa |
| 排除体积 excluded_volume | 71840 ų |
| 包络体积 envelope_volume | 87514 ų |
| 水化壳体积 shell_volume | 28264 ų |
| 包络直径 envelope_diameter | 91.3 Å |
| 壳层 Rg shell_rg | 33.14 Å |
| 包络 Rg envelope_rg | 25.99 Å |
| 形状 Rg shape_rg | 26.08 Å |
| 总 Rg total_rg | 27.08 Å |
| 总原子数 total_atoms | 3973 |
| 残基数 n_residues | 493 |
| 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 | 87.6 Å |
| Rg (实空间) rg_real | 27.12 Å |
| Rg 误差 (实空间) rg_real_error | 0.50 Å |
| I(0) (实空间) i0_real | 4.9210e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.3260e+05 |
| Rg (倒空间) rg_reciprocal | 27.15 Å |
| I(0) (倒空间) i0_reciprocal | 49210000.0000 |
| 解质量估计 total_estimate | 0.9047 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 86.1 Å |
| 偏度 Skewness skewness | 0.163 |
| 峰度 Kurtosis kurtosis | -0.618 |
| 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 | 16490000.0000 |
| 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: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.996 |
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) 10 domains
SCOP 2.08 (5 domains)
| 结构域编号 domain_id | d1mkma1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.33 — Transcriptional regulator IclR, N-terminal domain |
| 结构域编号 domain_id | d1mkma2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.110 — Profilin-like |
| 超家族 Superfamily superfamily | d.110.2 — GAF domain-like |
| 家族 Family family | d.110.2.2 — IclR ligand-binding domain-like |
| 结构域编号 domain_id | d1mkmb1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.33 — Transcriptional regulator IclR, N-terminal domain |
| 结构域编号 domain_id | d1mkmb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.110 — Profilin-like |
| 超家族 Superfamily superfamily | d.110.2 — GAF domain-like |
| 家族 Family family | d.110.2.2 — IclR ligand-binding domain-like |
| 结构域编号 domain_id | d1mkmb3 |
| 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 (5 domains)
| 结构域编号 domain_id | 1mkmA01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1mkmA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 640 — Single helix bin |
| 结构域编号 domain_id | 1mkmA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 450 — Beta-Lactamase |
| 同源超家族 H-superfamily homologous superfamily | 40 — GAF domain |
| 结构域编号 domain_id | 1mkmB01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1mkmB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 450 — Beta-Lactamase |
| 同源超家族 H-superfamily homologous superfamily | 40 — GAF domain |