1j35
Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein
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 | 1j35 |
| 沉积日期 deposition_date | 2003-01-20 |
| 结构标题 title | Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein |
| 关键词 keywords | MAGNESIUM ION, CALCIUM ION, GLA DOMAIN, Protein binding-Blood clotting COMPLEX; Protein binding/Blood clotting |
| 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 | 21.72 Å |
| 回转半径 Rg (电子) rg_electron | 20.92 Å |
| 零角强度 I(0) i0 | 23708400.00 |
| 分子量 molecular_weight | 35664.0 kDa |
| 排除体积 excluded_volume | 43726 ų |
| 包络体积 envelope_volume | 49721 ų |
| 水化壳体积 shell_volume | 20567 ų |
| 包络直径 envelope_diameter | 82.2 Å |
| 壳层 Rg shell_rg | 26.96 Å |
| 包络 Rg envelope_rg | 21.18 Å |
| 形状 Rg shape_rg | 20.92 Å |
| 总 Rg total_rg | 21.67 Å |
| 总原子数 total_atoms | 2490 |
| 残基数 n_residues | 286 |
| 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 | 80.0 Å |
| Rg (实空间) rg_real | 21.80 Å |
| Rg 误差 (实空间) rg_real_error | 0.64 Å |
| I(0) (实空间) i0_real | 2.3710e+07 |
| I(0) 误差 (实空间) i0_real_error | 3.4210e+05 |
| Rg (倒空间) rg_reciprocal | 21.78 Å |
| I(0) (倒空间) i0_reciprocal | 23710000.0000 |
| 解质量估计 total_estimate | 0.6366 |
| 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 | 22.7 Å |
| 偏度 Skewness skewness | 0.490 |
| 峰度 Kurtosis kurtosis | -0.074 |
| 角度范围 angular_range | — – 0.3650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 6867000.0000 |
| 实空间数据点数 n_real_points | 68 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.633; Stabil: 1.000; Sysdev: 0.207; Positv: 1.000; Valcen: 0.765; Smooth: 0.989 |
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) 5 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1j35a_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.169 — C-type lectin-like |
| 超家族 Superfamily superfamily | d.169.1 — C-type lectin-like |
| 家族 Family family | d.169.1.1 — C-type lectin domain |
| 结构域编号 domain_id | d1j35b_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.169 — C-type lectin-like |
| 超家族 Superfamily superfamily | d.169.1 — C-type lectin-like |
| 家族 Family family | d.169.1.1 — C-type lectin domain |
| 结构域编号 domain_id | d1j35c_ |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.32 — GLA-domain |
| 超家族 Superfamily superfamily | g.32.1 — GLA-domain |
| 家族 Family family | g.32.1.1 — GLA-domain |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1j35A00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 100 — Mannose-Binding Protein A; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Mannose-Binding Protein A, subunit A |
| 结构域编号 domain_id | 1j35B00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 100 — Mannose-Binding Protein A; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Mannose-Binding Protein A, subunit A |