1r7r
The crystal structure of murine p97/VCP at 3.6A
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 | 1r7r |
| 沉积日期 deposition_date | 2003-10-22 |
| 结构标题 title | The crystal structure of murine p97/VCP at 3.6A |
| 关键词 keywords | p97, VCP, AAA, CDC48, TRANSPORT PROTEIN; TRANSPORT PROTEIN |
| 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 | 30.41 Å |
| 回转半径 Rg (电子) rg_electron | 29.36 Å |
| 零角强度 I(0) i0 | 81913700.00 |
| 分子量 molecular_weight | 66441.0 kDa |
| 排除体积 excluded_volume | 81353 ų |
| 包络体积 envelope_volume | 121280 ų |
| 水化壳体积 shell_volume | 34428 ų |
| 包络直径 envelope_diameter | 96.5 Å |
| 壳层 Rg shell_rg | 36.48 Å |
| 包络 Rg envelope_rg | 29.56 Å |
| 形状 Rg shape_rg | 29.44 Å |
| 总 Rg total_rg | 29.86 Å |
| 总原子数 total_atoms | 4680 |
| 残基数 n_residues | 683 |
| 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 | 94.3 Å |
| Rg (实空间) rg_real | 30.32 Å |
| Rg 误差 (实空间) rg_real_error | 0.58 Å |
| I(0) (实空间) i0_real | 8.1910e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.3020e+06 |
| Rg (倒空间) rg_reciprocal | 30.36 Å |
| I(0) (倒空间) i0_reciprocal | 81920000.0000 |
| 解质量估计 total_estimate | 0.9122 |
| 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 | 38.1 Å |
| 偏度 Skewness skewness | 0.183 |
| 峰度 Kurtosis kurtosis | -0.579 |
| 角度范围 angular_range | — – 0.2600 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 12120000.0000 |
| 实空间数据点数 n_real_points | 53 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.961 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1r7ra1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.3 — Cdc48 N-terminal domain-like |
| 结构域编号 domain_id | d1r7ra2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.20 — Extended AAA-ATPase domain |
| 结构域编号 domain_id | d1r7ra3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.20 — Extended AAA-ATPase domain |
| 结构域编号 domain_id | d1r7ra4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.31 — Cdc48 domain 2-like |
| 超家族 Superfamily superfamily | d.31.1 — Cdc48 domain 2-like |
| 家族 Family family | d.31.1.1 — Cdc48 domain 2-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1r7rA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1r7rA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 330 — Vcp-like ATPase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1r7rA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1r7rA04 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 60 — |
| 结构域编号 domain_id | 1r7rA05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1r7rA06 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 8 — Helicase, Ruva Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 60 — |